diff options
| author | Larry Knox <lrknox@hdfgroup.org> | 2021-07-06 18:21:42 (GMT) |
|---|---|---|
| committer | Larry Knox <lrknox@hdfgroup.org> | 2021-07-06 18:21:42 (GMT) |
| commit | 820695a78e3a277daea1bdcbb8ad54b8ee6650a5 (patch) | |
| tree | fe7545305c0a77db3b9671e5a82fdffc4b2cc82e /java/src | |
| parent | 9f13ecfa2e93840d1cc45dbf0bfcf8b955814931 (diff) | |
| parent | 18bbd3f0a7f14adeebf8f342ed242ff191f9b7c5 (diff) | |
| download | hdf5-hdf5-1_12_1.zip hdf5-hdf5-1_12_1.tar.gz hdf5-hdf5-1_12_1.tar.bz2 | |
Merge remote-tracking branch 'origin/hdf5_1_12_1' into 1.12/master forhdf5-1_12_1
HDF5 1.12.1 release.
Diffstat (limited to 'java/src')
141 files changed, 6732 insertions, 1756 deletions
diff --git a/java/src/Makefile.am b/java/src/Makefile.am index b7ad4bd..98630e6 100644 --- a/java/src/Makefile.am +++ b/java/src/Makefile.am @@ -1,16 +1,15 @@ # # Copyright by The HDF Group. -# Copyright by the Board of Trustees of the University of Illinois. # All rights reserved. # # This file is part of HDF5. The full HDF5 copyright notice, including # terms governing use, modification, and redistribution, is contained in # the COPYING file, which can be found at the root of the source code -# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. +# distribution tree, or in https://www.hdfgroup.org/licenses. # If you do not have access to either file, you may request a copy from # help@hdfgroup.org. # -# +# # This makefile mostly just reinvokes make in the various subdirectories # but does so in the correct order. You can alternatively invoke make from # each subdirectory manually. diff --git a/java/src/Makefile.in b/java/src/Makefile.in index 5007086..0d5f362 100644 --- a/java/src/Makefile.in +++ b/java/src/Makefile.in @@ -16,17 +16,16 @@ # # Copyright by The HDF Group. -# Copyright by the Board of Trustees of the University of Illinois. # All rights reserved. # # This file is part of HDF5. The full HDF5 copyright notice, including # terms governing use, modification, and redistribution, is contained in # the COPYING file, which can be found at the root of the source code -# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. +# distribution tree, or in https://www.hdfgroup.org/licenses. # If you do not have access to either file, you may request a copy from # help@hdfgroup.org. # -# +# # This makefile mostly just reinvokes make in the various subdirectories # but does so in the correct order. You can alternatively invoke make from # each subdirectory manually. @@ -117,6 +116,7 @@ am__aclocal_m4_deps = $(top_srcdir)/m4/aclocal_cxx.m4 \ $(top_srcdir)/m4/ax_check_junit.m4 \ $(top_srcdir)/m4/ax_java_options.m4 \ $(top_srcdir)/m4/ax_jni_include_dir.m4 \ + $(top_srcdir)/m4/ax_prog_doxygen.m4 \ $(top_srcdir)/m4/ax_prog_jar.m4 \ $(top_srcdir)/m4/ax_prog_java.m4 \ $(top_srcdir)/m4/ax_prog_java_works.m4 \ @@ -255,7 +255,7 @@ AMTAR = @AMTAR@ # H5_CFLAGS holds flags that should be used when building hdf5, # but which should not be exported to h5cc for building other programs. -# AM_CFLAGS is an automake construct which should be used by Makefiles +# AM_CFLAGS is an automake construct which should be used by Makefiles # instead of CFLAGS, as CFLAGS is reserved solely for the user to define. # This applies to FCFLAGS, CXXFLAGS, CPPFLAGS, and LDFLAGS as well. AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@ @@ -280,6 +280,7 @@ CC = @CC@ CCDEPMODE = @CCDEPMODE@ CC_VERSION = @CC_VERSION@ CFLAGS = @CFLAGS@ +CLANG_SANITIZE_CHECKS = @CLANG_SANITIZE_CHECKS@ CODESTACK = @CODESTACK@ CONFIG_DATE = @CONFIG_DATE@ CONFIG_MODE = @CONFIG_MODE@ @@ -296,11 +297,54 @@ DEFAULT_API_VERSION = @DEFAULT_API_VERSION@ DEFS = @DEFS@ DEPDIR = @DEPDIR@ DEPRECATED_SYMBOLS = @DEPRECATED_SYMBOLS@ -DEV_WARNINGS = @DEV_WARNINGS@ +DESIRED_FILE_LOCKING = @DESIRED_FILE_LOCKING@ +DIAGS = @DIAGS@ DIRECT_VFD = @DIRECT_VFD@ DLLTOOL = @DLLTOOL@ +DOXYGEN_EXAMPLES_DIRECTORY = @DOXYGEN_EXAMPLES_DIRECTORY@ +DOXYGEN_EXTERNAL_SEARCH = @DOXYGEN_EXTERNAL_SEARCH@ +DOXYGEN_HTML_EXTRA_FILES = @DOXYGEN_HTML_EXTRA_FILES@ +DOXYGEN_HTML_EXTRA_STYLESHEET = @DOXYGEN_HTML_EXTRA_STYLESHEET@ +DOXYGEN_HTML_FOOTER = @DOXYGEN_HTML_FOOTER@ +DOXYGEN_HTML_HEADER = @DOXYGEN_HTML_HEADER@ +DOXYGEN_INCLUDE_ALIASES = @DOXYGEN_INCLUDE_ALIASES@ +DOXYGEN_INPUT_DIRECTORY = @DOXYGEN_INPUT_DIRECTORY@ +DOXYGEN_LAYOUT_FILE = @DOXYGEN_LAYOUT_FILE@ +DOXYGEN_MACRO_EXPANSION = @DOXYGEN_MACRO_EXPANSION@ +DOXYGEN_OPTIMIZE_OUTPUT_FOR_C = @DOXYGEN_OPTIMIZE_OUTPUT_FOR_C@ +DOXYGEN_OUTPUT_DIRECTORY = @DOXYGEN_OUTPUT_DIRECTORY@ +DOXYGEN_PACKAGE = @DOXYGEN_PACKAGE@ +DOXYGEN_PAPER_SIZE = @DOXYGEN_PAPER_SIZE@ +DOXYGEN_PROJECT_BRIEF = @DOXYGEN_PROJECT_BRIEF@ +DOXYGEN_PROJECT_LOGO = @DOXYGEN_PROJECT_LOGO@ +DOXYGEN_SEARCHENGINE_URL = @DOXYGEN_SEARCHENGINE_URL@ +DOXYGEN_SERVER_BASED_SEARCH = @DOXYGEN_SERVER_BASED_SEARCH@ +DOXYGEN_VERSION_STRING = @DOXYGEN_VERSION_STRING@ DSYMUTIL = @DSYMUTIL@ DUMPBIN = @DUMPBIN@ +DX_CONFIG = @DX_CONFIG@ +DX_DOCDIR = @DX_DOCDIR@ +DX_DOT = @DX_DOT@ +DX_DOXYGEN = @DX_DOXYGEN@ +DX_DVIPS = @DX_DVIPS@ +DX_EGREP = @DX_EGREP@ +DX_ENV = @DX_ENV@ +DX_FLAG_chi = @DX_FLAG_chi@ +DX_FLAG_chm = @DX_FLAG_chm@ +DX_FLAG_doc = @DX_FLAG_doc@ +DX_FLAG_dot = @DX_FLAG_dot@ +DX_FLAG_html = @DX_FLAG_html@ +DX_FLAG_man = @DX_FLAG_man@ +DX_FLAG_pdf = @DX_FLAG_pdf@ +DX_FLAG_ps = @DX_FLAG_ps@ +DX_FLAG_rtf = @DX_FLAG_rtf@ +DX_FLAG_xml = @DX_FLAG_xml@ +DX_HHC = @DX_HHC@ +DX_LATEX = @DX_LATEX@ +DX_MAKEINDEX = @DX_MAKEINDEX@ +DX_PDFLATEX = @DX_PDFLATEX@ +DX_PERL = @DX_PERL@ +DX_PROJECT = @DX_PROJECT@ ECHO_C = @ECHO_C@ ECHO_N = @ECHO_N@ ECHO_T = @ECHO_T@ @@ -334,6 +378,7 @@ H5_CPPFLAGS = @H5_CPPFLAGS@ H5_CXXFLAGS = @H5_CXXFLAGS@ H5_FCFLAGS = @H5_FCFLAGS@ H5_FORTRAN_SHARED = @H5_FORTRAN_SHARED@ +H5_IS_DARWIN = @H5_IS_DARWIN@ H5_JAVACFLAGS = @H5_JAVACFLAGS@ H5_JAVAFLAGS = @H5_JAVAFLAGS@ H5_JNIFLAGS = @H5_JNIFLAGS@ @@ -344,6 +389,7 @@ HAVE_DMALLOC = @HAVE_DMALLOC@ HAVE_Fortran_INTEGER_SIZEOF_16 = @HAVE_Fortran_INTEGER_SIZEOF_16@ HAVE_LIBHDFS = @HAVE_LIBHDFS@ HAVE_PTHREAD = @HAVE_PTHREAD@ +HDF5_DOXYGEN = @HDF5_DOXYGEN@ HDF5_HL = @HDF5_HL@ HDF5_INTERFACES = @HDF5_INTERFACES@ HDF5_TESTS = @HDF5_TESTS@ @@ -356,6 +402,7 @@ HL = @HL@ HL_FOR = @HL_FOR@ HSIZE_T = @HSIZE_T@ HSSIZE_T = @HSSIZE_T@ +IGNORE_DISABLED_FILE_LOCKS = @IGNORE_DISABLED_FILE_LOCKS@ INSTALL = @INSTALL@ INSTALL_DATA = @INSTALL_DATA@ INSTALL_PROGRAM = @INSTALL_PROGRAM@ @@ -393,6 +440,7 @@ MAKEINFO = @MAKEINFO@ MANIFEST_TOOL = @MANIFEST_TOOL@ MAP_API = @MAP_API@ MEMORYALLOCSANITYCHECK = @MEMORYALLOCSANITYCHECK@ +MIRROR_VFD = @MIRROR_VFD@ MKDIR_P = @MKDIR_P@ MPE = @MPE@ NM = @NM@ @@ -429,6 +477,7 @@ PATH_SEPARATOR = @PATH_SEPARATOR@ PREADWRITE = @PREADWRITE@ PROFILING = @PROFILING@ RANLIB = @RANLIB@ +RECURSIVE_RW_LOCKS = @RECURSIVE_RW_LOCKS@ ROOT = @ROOT@ ROS3_VFD = @ROS3_VFD@ RUNPARALLEL = @RUNPARALLEL@ @@ -440,6 +489,7 @@ SED = @SED@ SET_MAKE = @SET_MAKE@ SHELL = @SHELL@ SIZE_T = @SIZE_T@ +SRCDIR = '$(pkgpath)' STATIC_EXEC = @STATIC_EXEC@ STATIC_SHARED = @STATIC_SHARED@ STRICT_FORMAT_CHECKS = @STRICT_FORMAT_CHECKS@ @@ -452,6 +502,7 @@ TIME = @TIME@ TR = @TR@ TRACE_API = @TRACE_API@ UNAME_INFO = @UNAME_INFO@ +USE_FILE_LOCKING = @USE_FILE_LOCKING@ USE_FILTER_DEFLATE = @USE_FILTER_DEFLATE@ USE_FILTER_SZIP = @USE_FILTER_SZIP@ USINGMEMCHECKER = @USINGMEMCHECKER@ @@ -544,15 +595,15 @@ LIBH5_HL = $(top_builddir)/hl/src/libhdf5_hl.la LIBH5F_HL = $(top_builddir)/hl/fortran/src/libhdf5hl_fortran.la LIBH5CPP_HL = $(top_builddir)/hl/c++/src/libhdf5_hl_cpp.la -# Note that in svn revision 19400 the '/' after DESTDIR in H5* variables below -# has been removed. According to the official description of DESTDIR by Gnu at -# http://www.gnu.org/prep/standards/html_node/DESTDIR.html, DESTDIR is -# prepended to the normal and complete install path that it precedes for the -# purpose of installing in a temporary directory which is useful for building -# rpms and other packages. The '/' after ${DESTDIR} will be followed by another -# '/' at the beginning of the normal install path. When DESTDIR is empty the -# path then begins with '//', which is incorrect and causes problems at least for -# Cygwin. +# Note that in svn revision 19400 the '/' after DESTDIR in H5* variables below +# has been removed. According to the official description of DESTDIR by Gnu at +# http://www.gnu.org/prep/standards/html_node/DESTDIR.html, DESTDIR is +# prepended to the normal and complete install path that it precedes for the +# purpose of installing in a temporary directory which is useful for building +# rpms and other packages. The '/' after ${DESTDIR} will be followed by another +# '/' at the beginning of the normal install path. When DESTDIR is empty the +# path then begins with '//', which is incorrect and causes problems at least for +# Cygwin. # Scripts used to build examples # If only shared libraries have been installed, have h5cc build examples with @@ -656,7 +707,6 @@ hdf5_java_JAVA = \ hdf5_java_DATA = $(jarfile) WINDOWTITLE = 'HDF5 Java' DOCTITLE = '<h1>HDF5 Java Wrapper</h1>' -SRCDIR = '$(pkgpath)' CLEANFILES = classhdf5_java.stamp $(jarfile) $(JAVAROOT)/$(pkgpath)/callbacks/*.class $(JAVAROOT)/$(pkgpath)/exceptions/*.class $(JAVAROOT)/$(pkgpath)/structs/*.class $(JAVAROOT)/$(pkgpath)/*.class all: all-recursive @@ -1031,9 +1081,9 @@ uninstall-am: uninstall-hdf5_javaDATA uninstall-hdf5_javaJAVA # commands that should be executed even if a file with the same name already # exists. .PHONY: build-check-clean build-check-p build-check-s build-lib build-progs \ - build-tests check-clean check-install check-p check-s check-vfd \ - check-passthrough-vol install-doc lib progs tests uninstall-doc \ - _exec_check-s _test help + build-tests check-clean check-install check-p check-s check-vfd \ + check-passthrough-vol install-doc lib progs tests uninstall-doc \ + _exec_check-s _test help trace doxygen help: @$(top_srcdir)/bin/makehelp diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java index ff4ead3..af0a4b8 100644 --- a/java/src/hdf/hdf5lib/H5.java +++ b/java/src/hdf/hdf5lib/H5.java @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -216,7 +216,7 @@ import hdf.hdf5lib.structs.H5O_token_t; * exception handlers to print out the HDF-5 error stack. * <hr> * - * @version HDF5 1.12.0 <BR> + * @version HDF5 1.12.1 <BR> * <b>See also: <a href ="./hdf.hdf5lib.HDFArray.html"> hdf.hdf5lib.HDFArray</a> </b><BR> * <a href ="./hdf.hdf5lib.HDF5Constants.html"> hdf.hdf5lib.HDF5Constants</a><BR> * <a href ="./hdf.hdf5lib.HDF5CDataTypes.html"> hdf.hdf5lib.HDF5CDataTypes</a><BR> @@ -239,12 +239,16 @@ public class H5 implements java.io.Serializable { * * Make sure to update the versions number when a different library is used. */ - public final static int LIB_VERSION[] = { 1, 12, 0 }; + public final static int LIB_VERSION[] = { 1, 12, 1 }; + /** + * add system property to load library by path + */ public final static String H5PATH_PROPERTY_KEY = "hdf.hdf5lib.H5.hdf5lib"; - // add system property to load library by name from library path, via - // System.loadLibrary() + /** + * add system property to load library by name from library path, via System.loadLibrary() + */ public final static String H5_LIBRARY_NAME_PROPERTY_KEY = "hdf.hdf5lib.H5.loadLibraryName"; private static String s_libraryName; private static boolean isLibraryLoaded = false; @@ -257,6 +261,9 @@ public class H5 implements java.io.Serializable { loadH5Lib(); } + /** + * load native library + */ public static void loadH5Lib() { // Make sure that the library is loaded only once if (isLibraryLoaded) @@ -468,6 +475,35 @@ public class H5 implements java.io.Serializable { **/ public synchronized static native int H5get_libversion(int[] libversion) throws HDF5LibraryException; + /** + * H5set_free_list_limits + * Sets limits on the different kinds of free lists. Setting a value + * of -1 for a limit means no limit of that type. These limits are global + * for the entire library. Each "global" limit only applies to free lists + * of that type, so if an application sets a limit of 1 MB on each of the + * global lists, up to 3 MB of total storage might be allocated (1MB on + * each of regular, array and block type lists). + * + * The settings for block free lists are duplicated to factory free lists. + * Factory free list limits cannot be set independently currently. + * + * @param reg_global_lim + * The limit on all "regular" free list memory used + * @param reg_list_lim + * The limit on memory used in each "regular" free list + * @param arr_global_lim + * The limit on all "array" free list memory used + * @param arr_list_lim + * The limit on memory used in each "array" free list + * @param blk_global_lim + * The limit on all "block" free list memory used + * @param blk_list_lim + * The limit on memory used in each "block" free list + * @return a non-negative value if successful, along with the version information. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + */ public synchronized static native int H5set_free_list_limits(int reg_global_lim, int reg_list_lim, int arr_global_lim, int arr_list_lim, int blk_global_lim, int blk_list_lim) throws HDF5LibraryException; @@ -476,8 +512,8 @@ public class H5 implements java.io.Serializable { * * @param file_export_name * The file name to export data into. - * @param file_name - * The name of the HDF5 file containing the dataset. + * @param file_id + * The identifier of the HDF5 file containing the dataset. * @param object_path * The full path of the dataset to be exported. * @param binary_order @@ -489,10 +525,31 @@ public class H5 implements java.io.Serializable { * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ - public synchronized static native void H5export_dataset(String file_export_name, String file_name, + public synchronized static native void H5export_dataset(String file_export_name, long file_id, String object_path, int binary_order) throws HDF5LibraryException; /** + * H5export_attribute is a utility function to save data in a file. + * + * @param file_export_name + * The file name to export data into. + * @param dataset_id + * The identifier of the dataset containing the attribute. + * @param attribute_name + * The attribute to be exported. + * @param binary_order + * 99 - export data as text. + * 1 - export data as binary Native Order. + * 2 - export data as binary Little Endian. + * 3 - export data as binary Big Endian. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public synchronized static native void H5export_attribute(String file_export_name, long dataset_id, + String attribute_name, int binary_order) throws HDF5LibraryException; + + /** * H5is_library_threadsafe Checks to see if the library was built with thread-safety enabled. * * @return true if hdf5 library implements threadsafe @@ -1016,7 +1073,7 @@ public class H5 implements java.io.Serializable { /** * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with - * mem_type_id. The entire attribute is read into buf from the file. + * mem_type_id. The entire attribute is read into buffer from the file. * * @param attr_id * IN: Identifier of an attribute to read. @@ -1037,11 +1094,47 @@ public class H5 implements java.io.Serializable { public synchronized static native int H5Aread(long attr_id, long mem_type_id, byte[] obj, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static int H5Aread(long attr_id, long mem_type_id, byte[] buf) throws HDF5LibraryException, NullPointerException { return H5Aread(attr_id, mem_type_id, buf, true); } + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param obj + * Buffer to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static int H5Aread(long attr_id, long mem_type_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException { return H5Aread(attr_id, mem_type_id, obj, true); @@ -1141,63 +1234,343 @@ public class H5 implements java.io.Serializable { return status; } + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of double from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of double to store data read from the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static native int H5Aread_double(long attr_id, long mem_type_id, double[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of double from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of double to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static int H5Aread_double(long attr_id, long mem_type_id, double[] buf) throws HDF5LibraryException, NullPointerException { return H5Aread_double(attr_id, mem_type_id, buf, true); } + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of float from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of float to store data read from the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static native int H5Aread_float(long attr_id, long mem_type_id, float[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of float from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of float to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static int H5Aread_float(long attr_id, long mem_type_id, float[] buf) throws HDF5LibraryException, NullPointerException { return H5Aread_float(attr_id, mem_type_id, buf, true); } + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of int from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of int to store data read from the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static native int H5Aread_int(long attr_id, long mem_type_id, int[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of int from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of int to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static int H5Aread_int(long attr_id, long mem_type_id, int[] buf) throws HDF5LibraryException, NullPointerException { return H5Aread_int(attr_id, mem_type_id, buf, true); } + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of long from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of long to store data read from the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static native int H5Aread_long(long attr_id, long mem_type_id, long[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of long from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of long to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static int H5Aread_long(long attr_id, long mem_type_id, long[] buf) throws HDF5LibraryException, NullPointerException { return H5Aread_long(attr_id, mem_type_id, buf, true); } + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of String from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of String to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static native int H5Aread_reg_ref(long attr_id, long mem_type_id, String[] buf) throws HDF5LibraryException, NullPointerException; + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of short from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of short to store data read from the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static native int H5Aread_short(long attr_id, long mem_type_id, short[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of shortfrom the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of short to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static int H5Aread_short(long attr_id, long mem_type_id, short[] buf) throws HDF5LibraryException, NullPointerException { return H5Aread_short(attr_id, mem_type_id, buf, true); } + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of variable-lenght from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of variable-lenght to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static native int H5AreadVL(long attr_id, long mem_type_id, Object[] buf) throws HDF5LibraryException, NullPointerException; + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of String from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of String to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static native int H5Aread_string(long attr_id, long mem_type_id, String[] buf) throws HDF5LibraryException, NullPointerException; + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of variable-lenght strings from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of variable-lenght strings to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static native int H5Aread_VLStrings(long attr_id, long mem_type_id, Object[] buf) throws HDF5LibraryException, NullPointerException; + /** + * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is read into buffer of string from the file. + * + * @param attr_id + * IN: Identifier of an attribute to read. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * Buffer of string to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static native int H5AreadComplex(long attr_id, long mem_type_id, String[] buf) throws HDF5LibraryException, NullPointerException; @@ -1270,12 +1643,48 @@ public class H5 implements java.io.Serializable { public synchronized static native int H5Awrite(long attr_id, long mem_type_id, byte[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buf to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ public synchronized static int H5Awrite(long attr_id, long mem_type_id, byte[] buf) throws HDF5LibraryException, NullPointerException { return H5Awrite(attr_id, mem_type_id, buf, true); } + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buf to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param obj + * IN: Buffer with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ public synchronized static int H5Awrite(long attr_id, long mem_type_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException { @@ -1353,60 +1762,286 @@ public class H5 implements java.io.Serializable { return status; } + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of double to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of double with data to be written to the file. + * @param isCriticalPinning + * IN: request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ public synchronized static native int H5Awrite_double(long attr_id, long mem_type_id, double[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of double to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of double with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ public synchronized static int H5Awrite_double(long attr_id, long mem_type_id, double[] buf) throws HDF5LibraryException, NullPointerException { return H5Awrite_double(attr_id, mem_type_id, buf, true); } + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of float to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of float with data to be written to the file. + * @param isCriticalPinning + * IN: request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ public synchronized static native int H5Awrite_float(long attr_id, long mem_type_id, float[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of float to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of float with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ public synchronized static int H5Awrite_float(long attr_id, long mem_type_id, float[] buf) throws HDF5LibraryException, NullPointerException { return H5Awrite_float(attr_id, mem_type_id, buf, true); } + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of int to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of int with data to be written to the file. + * @param isCriticalPinning + * IN: request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ public synchronized static native int H5Awrite_int(long attr_id, long mem_type_id, int[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of int to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of int with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ public synchronized static int H5Awrite_int(long attr_id, long mem_type_id, int[] buf) throws HDF5LibraryException, NullPointerException { return H5Awrite_int(attr_id, mem_type_id, buf, true); } + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of long to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of long with data to be written to the file. + * @param isCriticalPinning + * IN: request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ public synchronized static native int H5Awrite_long(long attr_id, long mem_type_id, long[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of long to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of long with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ public synchronized static int H5Awrite_long(long attr_id, long mem_type_id, long[] buf) throws HDF5LibraryException, NullPointerException { return H5Awrite_long(attr_id, mem_type_id, buf, true); } + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of short to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of short with data to be written to the file. + * @param isCriticalPinning + * IN: request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ public synchronized static native int H5Awrite_short(long attr_id, long mem_type_id, short[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of short to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of short with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ public synchronized static int H5Awrite_short(long attr_id, long mem_type_id, short[] buf) throws HDF5LibraryException, NullPointerException { return H5Awrite_short(attr_id, mem_type_id, buf, true); } + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of string to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of string with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ public synchronized static native int H5Awrite_string(long attr_id, long mem_type_id, String[] buf) throws HDF5LibraryException, NullPointerException; + /** + * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with + * mem_type_id. The entire attribute is written from buffer of variable-lenght to the file. + * + * @param attr_id + * IN: Identifier of an attribute to write. + * @param mem_type_id + * IN: Identifier of the attribute datatype (in memory). + * @param buf + * IN: Buffer of variable-lenght with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data is null. + **/ public synchronized static native int H5AwriteVL(long attr_id, long mem_type_id, Object[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Awrite_VLStrings writes a variable length String dataset, specified by its identifier attr_id, from - * the application memory buffer buf into the file. + * the application memory buffer buffer of variable-lenght strings into the file. * * ---- contributed by Rosetta Biosoftware * @@ -1415,7 +2050,7 @@ public class H5 implements java.io.Serializable { * @param mem_type_id * Identifier of the memory datatype. * @param buf - * Buffer with data to be written to the file. + * Buffer of variable-lenght strings with data to be written to the file. * * @return a non-negative value if successful * @@ -1922,12 +2557,60 @@ public class H5 implements java.io.Serializable { long file_space_id, long xfer_plist_id, byte[] obj, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer buf. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException { return H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer buf. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param obj + * Buffer to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException { @@ -2043,65 +2726,411 @@ public class H5 implements java.io.Serializable { return status; } + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of type double. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of type double to store data read from the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static native int H5Dread_double(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, double[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of type double. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of double to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static int H5Dread_double(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, double[] buf) throws HDF5LibraryException, NullPointerException { return H5Dread_double(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of float. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of float to store data read from the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static native int H5Dread_float(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, float[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of float. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of float to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static int H5Dread_float(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, float[] buf) throws HDF5LibraryException, NullPointerException { return H5Dread_float(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of int. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of int to store data read from the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static native int H5Dread_int(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, int[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of int. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of int to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static int H5Dread_int(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, int[] buf) throws HDF5LibraryException, NullPointerException { return H5Dread_int(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of long. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of long to store data read from the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static native int H5Dread_long(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, long[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of long. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of long to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static int H5Dread_long(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, long[] buf) throws HDF5LibraryException, NullPointerException { return H5Dread_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of string. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of string to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static native int H5Dread_reg_ref(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException; + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of short. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of short to store data read from the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static native int H5Dread_short(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, short[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of short. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of short to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static int H5Dread_short(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, short[] buf) throws HDF5LibraryException, NullPointerException { return H5Dread_short(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of variable-lenght. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of variable-lenght to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static native int H5DreadVL(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, Object[] buf) throws HDF5LibraryException, NullPointerException; + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of string. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of string to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static native int H5Dread_string(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException; + /** + * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application + * memory buffer of variable-lenght strings. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of variable-lenght strings to store data read from the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - data buffer is null. + **/ public synchronized static native int H5Dread_VLStrings(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, Object[] buf) throws HDF5LibraryException, NullPointerException; @@ -2170,7 +3199,7 @@ public class H5 implements java.io.Serializable { /** * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer - * buf into the file. + * into the file. * * @param dataset_id * Identifier of the dataset read from. @@ -2198,12 +3227,60 @@ public class H5 implements java.io.Serializable { long file_space_id, long xfer_plist_id, byte[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ public synchronized static int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException { return H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param obj + * Buffer with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ public synchronized static int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException { @@ -2299,59 +3376,357 @@ public class H5 implements java.io.Serializable { return status; } + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of double with data to be written to the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ public synchronized static native int H5Dwrite_double(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, double[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of double with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ public synchronized static int H5Dwrite_double(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, double[] buf) throws HDF5LibraryException, NullPointerException { return H5Dwrite_double(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of float with data to be written to the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ public synchronized static native int H5Dwrite_float(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, float[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of float with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ public synchronized static int H5Dwrite_float(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, float[] buf) throws HDF5LibraryException, NullPointerException { return H5Dwrite_float(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of int with data to be written to the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ public synchronized static native int H5Dwrite_int(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, int[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of int with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ public synchronized static int H5Dwrite_int(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, int[] buf) throws HDF5LibraryException, NullPointerException { return H5Dwrite_int(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of long with data to be written to the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ public synchronized static native int H5Dwrite_long(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, long[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of long with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ public synchronized static int H5Dwrite_long(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, long[] buf) throws HDF5LibraryException, NullPointerException { return H5Dwrite_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of short with data to be written to the file. + * @param isCriticalPinning + * request lock on data reference. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ public synchronized static native int H5Dwrite_short(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, short[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of short with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ public synchronized static int H5Dwrite_short(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, short[] buf) throws HDF5LibraryException, NullPointerException { return H5Dwrite_short(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of string with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ public synchronized static native int H5Dwrite_string(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException; + /** + * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer + * into the file. + * + * @param dataset_id + * Identifier of the dataset read from. + * @param mem_type_id + * Identifier of the memory datatype. + * @param mem_space_id + * Identifier of the memory dataspace. + * @param file_space_id + * Identifier of the dataset's dataspace in the file. + * @param xfer_plist_id + * Identifier of a transfer property list for this I/O operation. + * @param buf + * Buffer of variable-length with data to be written to the file. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ public synchronized static native int H5DwriteVL(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, Object[] buf) throws HDF5LibraryException, NullPointerException; @@ -2628,7 +4003,7 @@ public class H5 implements java.io.Serializable { /** - * H5Epush2 pushes a new error record onto the error stack specified by estack_id. + * H5Epush pushes a new error record onto the error stack specified by estack_id. * * @param stack_id * IN: Error stack identifier. @@ -2657,6 +4032,31 @@ public class H5 implements java.io.Serializable { { H5Epush2(stack_id, file, func, line, cls_id, maj_id, min_id, msg); } + /** + * H5Epush2 pushes a new error record onto the error stack specified by estack_id. + * + * @param stack_id + * IN: Error stack identifier. + * @param file + * IN: Name of the file in which the error was detected. + * @param func + * IN: Name of the function in which the error was detected. + * @param line + * IN: Line number within the file at which the error was detected. + * @param cls_id + * IN: Error class identifier. + * @param maj_id + * IN: Major error identifier. + * @param min_id + * IN: Minor error identifier. + * @param msg + * IN: Error description string. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - file, func, or msg is null. + **/ public synchronized static native void H5Epush2(long stack_id, String file, String func, int line, long cls_id, long maj_id, long min_id, String msg) throws HDF5LibraryException, NullPointerException; @@ -2714,6 +4114,24 @@ public class H5 implements java.io.Serializable { { H5Ewalk2(stack_id, direction, func, client_data); } + /** + * H5Ewalk2 walks the error stack specified by estack_id for the current thread and calls the + * function specified in func for each error along the way. + * + * @param stack_id + * IN: Error stack identifier. + * @param direction + * IN: Direction in which the error stack is to be walked. + * @param func + * IN: Function to be called for each error encountered. + * @param client_data + * IN: Data to be passed with func. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - func is null. + **/ public synchronized static native void H5Ewalk2(long stack_id, long direction, H5E_walk_cb func, H5E_walk_t client_data) throws HDF5LibraryException, NullPointerException; @@ -2950,6 +4368,19 @@ public class H5 implements java.io.Serializable { private synchronized static native long _H5Fget_create_plist(long file_id) throws HDF5LibraryException; + /** + * H5Fget_filesize retrieves the file size of the HDF5 file. This function + * is called after an existing file is opened in order + * to learn the true size of the underlying file. + * + * @param file_id + * IN: File identifier for a currently-open HDF5 file + * + * @return the file size of the HDF5 file + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native long H5Fget_filesize(long file_id) throws HDF5LibraryException; /** @@ -3598,37 +5029,118 @@ public class H5 implements java.io.Serializable { return H5Gget_obj_info_all(loc_id, name, objNames, objTypes, null, null, tokens, HDF5Constants.H5_INDEX_NAME); } - public synchronized static int H5Gget_obj_info_all(long loc_id, String name, String[] oname, int[] otype, + /** + * retrieves information of all objects under the group (name) located in the file or group specified by loc_id. + * + * @param loc_id + * IN: File or group identifier + * @param name + * IN: Name of group for which information is to be retrieved + * @param objNames + * OUT: Names of all objects under the group, name. + * @param objTypes + * OUT: Types of all objects under the group, name. + * @param ltype + * OUT: Link type + * @param tokens + * OUT: Object token of all objects under the group, name. + * @param indx_type + * IN: Index type for iterate + * + * @return the number of items found + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + */ + public synchronized static int H5Gget_obj_info_all(long loc_id, String name, String[] objNames, int[] objTypes, int[] ltype, H5O_token_t[] tokens, int indx_type) throws HDF5LibraryException, NullPointerException { - return H5Gget_obj_info_full(loc_id, name, oname, otype, ltype, null, tokens, indx_type, -1); + return H5Gget_obj_info_full(loc_id, name, objNames, objTypes, ltype, null, tokens, indx_type, -1); } - public synchronized static int H5Gget_obj_info_all(long loc_id, String name, String[] oname, int[] otype, + /** + * retrieves information of all objects under the group (name) located in the file or group specified by loc_id. + * + * @param loc_id + * IN: File or group identifier + * @param name + * IN: Name of group for which information is to be retrieved + * @param objNames + * OUT: Names of all objects under the group, name. + * @param objTypes + * OUT: Types of all objects under the group, name. + * @param ltype + * OUT: Link type + * @param fno + * OUT: File number + * @param tokens + * OUT: Object token of all objects under the group, name. + * @param indx_type + * IN: Index type for iterate + * + * @return the number of items found + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + */ + public synchronized static int H5Gget_obj_info_all(long loc_id, String name, String[] objNames, int[] objTypes, int[] ltype, long[] fno, H5O_token_t[] tokens, int indx_type) throws HDF5LibraryException, NullPointerException { - return H5Gget_obj_info_full(loc_id, name, oname, otype, ltype, fno, tokens, indx_type, -1); + return H5Gget_obj_info_full(loc_id, name, objNames, objTypes, ltype, fno, tokens, indx_type, -1); } - public synchronized static int H5Gget_obj_info_full(long loc_id, String name, String[] oname, int[] otype, + /** + * retrieves information of all objects under the group (name) located in the file or group specified by loc_id. + * + * @param loc_id + * IN: File or group identifier + * @param name + * IN: Name of group for which information is to be retrieved + * @param objNames + * OUT: Names of all objects under the group, name. + * @param objTypes + * OUT: Types of all objects under the group, name. + * @param ltype + * OUT: Link type + * @param fno + * OUT: File number + * @param tokens + * OUT: Object token of all objects under the group, name. + * @param indx_type + * IN: Index type for iterate + * @param indx_order + * IN: Index order for iterate + * + * @return the number of items found + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + */ + public synchronized static int H5Gget_obj_info_full(long loc_id, String name, String[] objNames, int[] objTypes, int[] ltype, long[] fno, H5O_token_t[] tokens, int indx_type, int indx_order) throws HDF5LibraryException, NullPointerException { - if (oname == null) { + if (objNames == null) { throw new NullPointerException("H5Gget_obj_info_full(): name array is null"); } - if (otype == null) { + if (objTypes == null) { throw new NullPointerException("H5Gget_obj_info_full(): object type array is null"); } - if (oname.length == 0) { + if (objNames.length == 0) { throw new HDF5LibraryException("H5Gget_obj_info_full(): array size is zero"); } - if (oname.length != otype.length) { + if (objNames.length != objTypes.length) { throw new HDF5LibraryException("H5Gget_obj_info_full(): name and type array sizes are different"); } if (ltype == null) - ltype = new int[otype.length]; + ltype = new int[objTypes.length]; if (fno == null) fno = new long[tokens.length]; @@ -3639,15 +5151,15 @@ public class H5 implements java.io.Serializable { if (indx_order < 0) indx_order = HDF5Constants.H5_ITER_INC; - log.trace("H5Gget_obj_info_full: oname_len={}", oname.length); - int status = H5Gget_obj_info_full(loc_id, name, oname, otype, ltype, fno, tokens, oname.length, indx_type, + log.trace("H5Gget_obj_info_full: objNames_len={}", objNames.length); + int status = H5Gget_obj_info_full(loc_id, name, objNames, objTypes, ltype, fno, tokens, objNames.length, indx_type, indx_order); - for (int indx = 0; indx < oname.length; indx++) - log.trace("H5Gget_obj_info_full: oname={}", oname[indx]); + for (int indx = 0; indx < objNames.length; indx++) + log.trace("H5Gget_obj_info_full: objNames={}", objNames[indx]); return status; } - private synchronized static native int H5Gget_obj_info_full(long loc_id, String name, String[] oname, int[] otype, + private synchronized static native int H5Gget_obj_info_full(long loc_id, String name, String[] objNames, int[] objTypes, int[] ltype, long[] fno, H5O_token_t[] tokens, int n, int indx_type, int indx_order) throws HDF5LibraryException, NullPointerException; @@ -3663,9 +5175,9 @@ public class H5 implements java.io.Serializable { * @param idx * IN: the index of the object to iterate. * @param oname - * the name of the object [OUT] + * OUT: the name of the object * @param type - * the type of the object [OUT] + * OUT: the type of the object * * @return non-negative if successful, -1 if not. * @@ -3866,13 +5378,40 @@ public class H5 implements java.io.Serializable { // // // //////////////////////////////////////////////////////////// + /** + * H5Iget_file_id obtains the file ID specified by the identifier, obj_id. + * + * @param obj_id + * IN: Identifier of the object. + * + * @return the file ID. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native long H5Iget_file_id(long obj_id) throws HDF5LibraryException; + /** + * H5Iget_name_long retrieves the name of an object specified by the identifier, obj_id. + * @deprecated + * + * @param obj_id + * IN: Identifier of the object. + * @param name + * OUT: Attribute name buffer. + * @param size + * IN: Maximum length of the name to retrieve. + * + * @return the length of the name retrieved. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ @Deprecated public synchronized static native long H5Iget_name_long(long obj_id, String[] name, long size) throws HDF5LibraryException, NullPointerException; /** - * H5Iget_name_str retrieves the name of an object specified by the identifier, obj_id. + * H5Iget_name retrieves the name of an object specified by the identifier, obj_id. * * @param obj_id * IN: Identifier of the object. @@ -3885,10 +5424,44 @@ public class H5 implements java.io.Serializable { public synchronized static native String H5Iget_name(long obj_id) throws HDF5LibraryException; + /** + * H5Iget_ref obtains the number of references outstanding specified by the identifier, obj_id. + * + * @param obj_id + * IN: Identifier of the object. + * + * @return the reference count. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native int H5Iget_ref(long obj_id) throws HDF5LibraryException, NullPointerException; + /** + * H5Idec_ref decrements the reference count specified by the identifier, obj_id. + * If the reference count for an ID reaches zero, the object will be closed. + * + * @param obj_id + * IN: Identifier of the object. + * + * @return the reference count. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native int H5Idec_ref(long obj_id) throws HDF5LibraryException, NullPointerException; + /** + * H5Iinc_ref increments the reference count specified by the identifier, obj_id. + * + * @param obj_id + * IN: Identifier of the object. + * + * @return the reference count. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native int H5Iinc_ref(long obj_id) throws HDF5LibraryException, NullPointerException; /** @@ -5179,7 +6752,7 @@ public class H5 implements java.io.Serializable { return id; } - public synchronized static native long _H5Oopen_by_idx(long loc_id, String group_name, + private synchronized static native long _H5Oopen_by_idx(long loc_id, String group_name, int idx_type, int order, long n, long lapl_id) throws HDF5LibraryException, NullPointerException; /** @@ -5210,8 +6783,30 @@ public class H5 implements java.io.Serializable { **/ public synchronized static native void H5Orefresh(long object_id) throws HDF5LibraryException; + /** + * H5Odisable_mdc_flushes corks an object, keeping dirty entries associated with the object in the metadata cache. + * + * @param object_id + * IN: Identifier of the object to be corked. + **/ public synchronized static native void H5Odisable_mdc_flushes(long object_id); + /** + * H5Oenable_mdc_flushes uncorks an object, keeping dirty entries associated with the object in the metadata cache. + * + * @param object_id + * IN: Identifier of the object to be uncorked. + **/ public synchronized static native void H5Oenable_mdc_flushes(long object_id); + /** + * H5Oare_mdc_flushes_disabled retrieve the object's "cork" status. + * + * @param object_id + * IN: Identifier of the object to be flushed. + * + * @return the cork status + * TRUE if mdc flushes for the object is disabled + * FALSE if mdc flushes for the object is not disabled + **/ public synchronized static native boolean H5Oare_mdc_flushes_disabled(long object_id); // /////// unimplemented //////// @@ -5364,6 +6959,7 @@ public class H5 implements java.io.Serializable { * IN: First property object to be compared * @param plid2 * IN: Second property object to be compared + * * @return positive value if equal; zero if unequal, a negative value if failed * * @exception HDF5LibraryException @@ -5371,6 +6967,19 @@ public class H5 implements java.io.Serializable { */ public synchronized static native int H5Pequal(long plid1, long plid2) throws HDF5LibraryException; + /** + * H5Pequal determines if two property lists or classes are equal + * + * @param plid1 + * IN: First property object to be compared + * @param plid2 + * IN: Second property object to be compared + * + * @return TRUE if equal, FALSE if unequal + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + */ public static boolean H5P_equal(long plid1, long plid2) throws HDF5LibraryException { if (H5Pequal(plid1, plid2) == 1) return true; @@ -5456,7 +7065,7 @@ public class H5 implements java.io.Serializable { return _H5Pclose_class(plid); } - public synchronized static native int _H5Pclose_class(long plid) throws HDF5LibraryException; + private synchronized static native int _H5Pclose_class(long plid) throws HDF5LibraryException; /** * H5Pclose terminates access to a property list. @@ -5524,6 +7133,19 @@ public class H5 implements java.io.Serializable { // Define property list iteration function type // typedef herr_t (*H5P_iterate_t)(hid_t id, const char *name, void *iter_data); + /** + * H5Pcreate_class_nocb creates an new property class with no callback functions. + * + * @param parent_class + * IN: Identifier of the parent property class. + * @param name + * IN: Name of the property class. + * + * @return a property list identifier if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public static long H5Pcreate_class_nocb(long parent_class, String name) throws HDF5LibraryException { long id = _H5Pcreate_class_nocb(parent_class, name); if (id > 0) { @@ -5550,17 +7172,69 @@ public class H5 implements java.io.Serializable { // private synchronized static native long _H5Pcreate_class(long parent_class, String name, H5P_cls_create_func_cb create_op, H5P_cls_create_func_t create_data, // H5P_cls_copy_func_cb copy_op, H5P_cls_copy_func_t copy_data, H5P_cls_close_func_cb close_op, H5P_cls_close_func_t close_data) throws HDF5LibraryException; + /** + * H5Pregister2_nocb registers a property list with no callback functions. + * + * @param plist_class + * IN: Identifier of the property list. + * @param name + * IN: Name of the property. + * @param size + * IN: Size the property value. + * @param def_value + * IN: Defaul value of the property + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native void H5Pregister2_nocb(long plist_class, String name, long size, byte[] def_value) throws HDF5LibraryException; // public synchronized static native void H5Pregister2(long plist_class, String name, long size, byte[] def_value, H5P_prp_create_func_cb prp_create, H5P_prp_set_func_cb prp_set, // H5P_prp_get_func_cb prp_get, H5P_prp_delete_func_cb prp_delete, H5P_prp_copy_func_cb prp_copy, H5P_prp_compare_func_cb prp_cmp, H5P_prp_close_func_cb prp_close) throws HDF5LibraryException; + /** + * H5Pinsert2_nocb inserts a property list with no callback functions. + * + * @param plist + * IN: Identifier of the property list. + * @param name + * IN: Name of the property. + * @param size + * IN: Size the property value. + * @param value + * IN: Defaul value of the property + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native void H5Pinsert2_nocb(long plist, String name, long size, byte[] value) throws HDF5LibraryException; // public synchronized static native void H5Pinsert2(long plist, String name, long size, byte[] value, H5P_prp_set_func_cb prp_set, H5P_prp_get_func_cb prp_get, // H5P_prp_delete_func_cb prp_delete, H5P_prp_copy_func_cb prp_copy, H5P_prp_compare_func_cb prp_cmp, H5P_prp_close_func_cb prp_close) throws HDF5LibraryException; + /** + * H5Piterate iterates over the properties in a property list or class + * + * @param plist + * IN: ID of property object to iterate over + * @param idx + * IN/OUT: index of the property to begin with + * @param op + * IN: function to be called with each property iterated over. + * @param op_data + * IN: iteration data from user + * + * @return + * the return value of the last call to op if it was non-zero, + * zero if all properties have been processed + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - size is null. + * + **/ public synchronized static native int H5Piterate(long plist, int[] idx, H5P_iterate_cb op, H5P_iterate_t op_data) throws HDF5LibraryException; // /////// Object creation property list (OCPL) routines /////// @@ -5573,7 +7247,7 @@ public class H5 implements java.io.Serializable { * @param attributes * The maximun and minimum no. of attributes to be stored. * - * <pre> + * <pre> * attributes[0] = The maximum number of attributes to be stored in compact storage * attributes[1] = The minimum number of attributes to be stored in dense storage * </pre> @@ -5673,6 +7347,51 @@ public class H5 implements java.io.Serializable { public synchronized static native void H5Pset_obj_track_times(long ocpl_id, boolean track_times) throws HDF5LibraryException; + /** + * H5Pmodify_filter modifies the specified FILTER in the transient or permanent output filter pipeline + * depending on whether PLIST is a dataset creation or dataset + * transfer property list. The FLAGS argument specifies certain + * general properties of the filter and is documented below. + * The CD_VALUES is an array of CD_NELMTS integers which are + * auxiliary data for the filter. The integer vlues will be + * stored in the dataset object header as part of the filter + * information. + *<p> + * The FLAGS argument is a bit vector of the following fields: + *<p> + * H5Z_FLAG_OPTIONAL(0x0001) + * If this bit is set then the filter is optional. If the + * filter fails during an H5Dwrite() operation then the filter + * is just excluded from the pipeline for the chunk for which it + * failed; the filter will not participate in the pipeline + * during an H5Dread() of the chunk. If this bit is clear and + * the filter fails then the entire I/O operation fails. + * If this bit is set but encoding is disabled for a filter, + * attempting to write will generate an error. + *<p> + * Note: This function currently supports only the permanent filter + * pipeline. That is, PLIST_ID must be a dataset creation + * property list. + * + * @param plist + * IN: Property list identifier. + * @param filter + * IN: Filter to be modified to the pipeline. + * @param flags + * IN: Bit vector specifying certain general properties of the filter. + * @param cd_nelmts + * IN: Number of elements in cd_values + * @param cd_values + * IN: Auxiliary data for the filter. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name or an array is null. + * + **/ public synchronized static native int H5Pmodify_filter(long plist, long filter, int flags, long cd_nelmts, int[] cd_values) throws HDF5LibraryException, NullPointerException; @@ -5844,9 +7563,37 @@ public class H5 implements java.io.Serializable { throws HDF5LibraryException, NullPointerException; + /** + * H5Pall_filters_avail query to verify that all the filters set + * in the dataset creation property list are available currently. + * + * @param dcpl_id + * IN: Property list identifier. + * + * @return + * TRUE if all filters available + * FALSE if one or more filters not currently available. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native boolean H5Pall_filters_avail(long dcpl_id) throws HDF5LibraryException, NullPointerException; + /** + * H5Premove_filter deletes a filter from the dataset creation property list; + * deletes all filters if filter is H5Z_FILTER_NONE + * + * @param obj_id + * IN: Property list identifier. + * @param filter + * IN: Filter identifier. + * + * @return a non-negative value and the size of the user block; if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native int H5Premove_filter(long obj_id, long filter) throws HDF5LibraryException; /** @@ -5864,6 +7611,18 @@ public class H5 implements java.io.Serializable { **/ public synchronized static native int H5Pset_deflate(long plist, int level) throws HDF5LibraryException; + /** + * H5Pset_fletcher32 sets Fletcher32 checksum of EDC for a dataset creation + * property list or group creation property list. + * + * @param plist + * IN: Property list identifier. + * + * @return a non-negative value and the size of the user block; if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native int H5Pset_fletcher32(long plist) throws HDF5LibraryException, NullPointerException; @@ -6334,11 +8093,35 @@ public class H5 implements java.io.Serializable { */ public synchronized static native long H5Pget_driver(long plid) throws HDF5LibraryException; - public synchronized static native long H5Pget_family_offset(long fapl_id) throws HDF5LibraryException, - NullPointerException; + /** + * H5Pget_family_offset gets offset for family driver. + * + * @param fapl_id + * IN: File access property list identifier + * + * @return the offset. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * + **/ + public synchronized static native long H5Pget_family_offset(long fapl_id) throws HDF5LibraryException; - public synchronized static native int H5Pset_family_offset(long fapl_id, long offset) throws HDF5LibraryException, - NullPointerException; + /** + * H5Pset_family_offset sets the offset for family driver. + * + * @param fapl_id + * IN: File access property list identifier + * @param offset + * IN: the offset value + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * + **/ + public synchronized static native int H5Pset_family_offset(long fapl_id, long offset) throws HDF5LibraryException; /** * Retrieves the maximum possible number of elements in the meta data cache and the maximum possible number of bytes @@ -6389,9 +8172,8 @@ public class H5 implements java.io.Serializable { double rdcc_w0) throws HDF5LibraryException; /** - * H5Pget_mdc_config gets the initial metadata cache configuration contained in a file access property list and - * loads it into the instance of H5AC_cache_config_t pointed to by the config_ptr parameter. This configuration is - * used when the file is opened. + * H5Pget_mdc_config gets the initial metadata cache configuration contained in a file access property list. + * This configuration is used when the file is opened. * * @param plist_id * IN: Identifier of the file access property list. @@ -6403,6 +8185,19 @@ public class H5 implements java.io.Serializable { **/ public synchronized static native H5AC_cache_config_t H5Pget_mdc_config(long plist_id) throws HDF5LibraryException; + /** + * H5Pset_mdc_config sets the initial metadata cache configuration contained in a file access property list and + * loads it into the instance of H5AC_cache_config_t pointed to by the config_ptr parameter. This configuration is + * used when the file is opened. + * + * @param plist_id + * IN: Identifier of the file access property list. + * @param config_ptr + * IN: H5AC_cache_config_t, the initial metadata cache configuration. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native void H5Pset_mdc_config(long plist_id, H5AC_cache_config_t config_ptr) throws HDF5LibraryException; @@ -6437,10 +8232,35 @@ public class H5 implements java.io.Serializable { public synchronized static native int H5Pset_gc_references(long fapl_id, boolean gc_ref) throws HDF5LibraryException; - public synchronized static native int H5Pget_fclose_degree(long plist_id) throws HDF5LibraryException, + /** + * H5Pget_fclose_degree returns the degree for the file close behavior for a file access + * property list. + * + * @param fapl_id + * IN File access property list + * + * @return the degree for the file close behavior + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public synchronized static native int H5Pget_fclose_degree(long fapl_id) throws HDF5LibraryException, NullPointerException; - public synchronized static native int H5Pset_fclose_degree(long plist, int degree) throws HDF5LibraryException, + /** + * H5Pset_fclose_degree sets the degree for the file close behavior. + * + * @param fapl_id + * IN File access property list + * @param degree + * IN the degree for the file close behavior + * + * @return non-negative if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public synchronized static native int H5Pset_fclose_degree(long fapl_id, int degree) throws HDF5LibraryException, NullPointerException; /** @@ -6471,8 +8291,40 @@ public class H5 implements java.io.Serializable { **/ public synchronized static native void H5Pset_meta_block_size(long fapl_id, long size) throws HDF5LibraryException; + /** + * H5Pget_sieve_buf_size retrieves the current settings for the data sieve buffer size + * property from a file access property list. + * + * @param fapl_id + * IN: Identifier for property list to query. + * + * @return a non-negative value and the size of the user block; if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native long H5Pget_sieve_buf_size(long fapl_id) throws HDF5LibraryException; + /** + * H5Pset_sieve_buf_size Sets the maximum size of the data seive buffer used for file + * drivers which are capable of using data sieving. The data sieve + * buffer is used when performing I/O on datasets in the file. Using a + * buffer which is large anough to hold several pieces of the dataset + * being read in for hyperslab selections boosts performance by quite a + * bit. + * <p> + * The default value is set to 64KB, indicating that file I/O for raw data + * reads and writes will occur in at least 64KB blocks. Setting the value to 0 + * with this function will turn off the data sieving + * + * @param fapl_id + * IN: Identifier of property list to modify. + * @param size + * IN: maximum size of the data seive buffer. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native void H5Pset_sieve_buf_size(long fapl_id, long size) throws HDF5LibraryException; /** @@ -6687,6 +8539,55 @@ public class H5 implements java.io.Serializable { public synchronized static native void H5Pset_evict_on_close(long fapl_id, boolean evict_on_close) throws HDF5LibraryException; + /** + * H5Pget_use_file_locking retrieves whether we are using file locking. + * + * @param fapl_id + * IN: File access property list identifier + * + * @return indication if file locking is used. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * + **/ + public synchronized static native boolean H5Pget_use_file_locking(long fapl_id) + throws HDF5LibraryException; + + /** + * H5Pget_use_file_locking retrieves whether we ignore file locks when they are disabled. + * + * @param fapl_id + * IN: File access property list identifier + * + * @return indication if file locking is ignored. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * + **/ + public synchronized static native boolean H5Pget_ignore_disabled_file_locking(long fapl_id) + throws HDF5LibraryException; + + /** + * H5Pset_file_locking sets parameters related to file locking. + * + * @param fapl_id + * IN: File access property list identifier + * + * @param use_file_locking + * IN: Whether the library will use file locking when opening files (mainly for SWMR semantics). + * + * @param ignore_when_disabled + * IN: Whether file locking will be ignored when disabled on a file system (useful for Lustre). + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * + **/ + public synchronized static native void H5Pset_file_locking(long fapl_id, boolean use_file_locking, boolean ignore_when_disabled) + throws HDF5LibraryException; + // ///// unimplemented ///// // herr_t H5Pset_vol(hid_t plist_id, hid_t new_vol_id, const void *new_vol_info); // herr_t H5Pget_vol_id(hid_t plist_id, hid_t *vol_id); @@ -6767,6 +8668,25 @@ public class H5 implements java.io.Serializable { public synchronized static native int H5Pset_chunk(long plist, int ndims, byte[] dim) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; + /** + * H5Pset_chunk sets the size of the chunks used to store a chunked layout dataset. + * + * @param plist + * IN: Identifier for property list to query. + * @param ndims + * IN: The number of dimensions of each chunk. + * @param dim + * IN: An array containing the size of each chunk. + * + * @return a non-negative value if successful + * + * @exception HDF5Exception + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - dims array is null. + * @exception IllegalArgumentException + * - dims <=0 + **/ public synchronized static int H5Pset_chunk(long plist, int ndims, long[] dim) throws HDF5Exception, NullPointerException, IllegalArgumentException { if (dim == null) { @@ -7002,9 +8922,37 @@ public class H5 implements java.io.Serializable { **/ public synchronized static native int H5Pget_external_count(long plist) throws HDF5LibraryException; + /** + * H5Pset_szip Sets up the use of the szip filter. + * + * @param plist + * IN: Dataset creation property list identifier. + * @param options_mask + * IN: Bit vector specifying certain general properties of the filter. + * @param pixels_per_block + * IN: Number of pixels in blocks + * + * @return a non-negative value if successful; otherwise returns a negative value. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * + **/ public synchronized static native int H5Pset_szip(long plist, int options_mask, int pixels_per_block) throws HDF5LibraryException, NullPointerException; + /** + * H5Pset_shuffle Sets up the use of the shuffle filter. + * + * @param plist_id + * IN: Dataset creation property list identifier. + * + * @return a non-negative value if successful; otherwise returns a negative value. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * + **/ public synchronized static native int H5Pset_shuffle(long plist_id) throws HDF5LibraryException, NullPointerException; @@ -7132,20 +9080,91 @@ public class H5 implements java.io.Serializable { return retVal; } + /** + * H5Pset_fill_value checks if the fill value is defined for a dataset creation property list. + * + * @param plist_id + * IN: Property list identifier. + * @param status + * IN: The fill value setting: + * H5D_FILL_VALUE_UNDEFINED + * H5D_FILL_VALUE_DEFAULT + * H5D_FILL_VALUE_USER_DEFINED + * H5D_FILL_VALUE_ERROR + * + * @return a non-negative value if successful + * + * @exception HDF5Exception + * - Error converting data array + **/ public synchronized static native int H5Pfill_value_defined(long plist_id, int[] status) throws HDF5LibraryException, NullPointerException; + /** + * H5Pset_alloc_time Gets space allocation time for dataset during creation. + * + * @param plist_id + * IN: Dataset creation property list identifier. + * @param alloc_time + * OUT: allocation time. + * + * @return a non-negative value if successful; otherwise returns a negative value. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * + **/ public synchronized static native int H5Pget_alloc_time(long plist_id, int[] alloc_time) throws HDF5LibraryException, NullPointerException; + /** + * H5Pset_alloc_time Sets space allocation time for dataset during creation. + * + * @param plist_id + * IN: Dataset creation property list identifier. + * @param alloc_time + * IN: allocation time. + * + * @return a non-negative value if successful; otherwise returns a negative value. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * + **/ public synchronized static native int H5Pset_alloc_time(long plist_id, int alloc_time) throws HDF5LibraryException, NullPointerException; - public synchronized static native int H5Pget_fill_time(long plist_id, int[] fill_time) throws HDF5LibraryException, - NullPointerException; + /** + * H5Pset_fill_time Gets fill value writing time. + * + * @param plist_id + * IN: Dataset creation property list identifier. + * @param fill_time + * OUT: fill time. + * + * @return a non-negative value if successful; otherwise returns a negative value. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * + **/ + public synchronized static native int H5Pget_fill_time(long plist_id, int[] fill_time) throws HDF5LibraryException; - public synchronized static native int H5Pset_fill_time(long plist_id, int fill_time) throws HDF5LibraryException, - NullPointerException; + /** + * H5Pset_fill_time Sets the fill value writing time. + * + * @param plist_id + * IN: Dataset creation property list identifier. + * @param fill_time + * IN: fill time. + * + * @return a non-negative value if successful; otherwise returns a negative value. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * + **/ + public synchronized static native int H5Pset_fill_time(long plist_id, int fill_time) throws HDF5LibraryException; /** * H5Pset_chunk_opts Sets the edge chunk option in a dataset creation property list. @@ -7445,6 +9464,20 @@ public class H5 implements java.io.Serializable { public synchronized static native int H5Pget_buffer(long plist, byte[] tconv, byte[] bkg) throws HDF5LibraryException, IllegalArgumentException; + /** + * H5Pget_buffer_size gets type conversion and background buffer size, in bytes, if successful; + * otherwise 0 on failure. + * + * @param plist + * Identifier for the dataset transfer property list. + * + * @return buffer size, in bytes, if successful; otherwise 0 on failure + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception IllegalArgumentException + * - plist is invalid. + **/ public synchronized static native long H5Pget_buffer_size(long plist) throws HDF5LibraryException, IllegalArgumentException; @@ -7475,11 +9508,33 @@ public class H5 implements java.io.Serializable { public synchronized static native void H5Pset_buffer_size(long plist, long size) throws HDF5LibraryException, IllegalArgumentException; - public synchronized static native int H5Pget_edc_check(long plist) throws HDF5LibraryException, - NullPointerException; + /** + * H5Pget_edc_check gets the error-detecting algorithm in use. + * + * @param plist + * Identifier for the dataset transfer property list. + * + * @return the error-detecting algorithm + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public synchronized static native int H5Pget_edc_check(long plist) throws HDF5LibraryException; - public synchronized static native int H5Pset_edc_check(long plist, int check) throws HDF5LibraryException, - NullPointerException; + /** + * H5Pset_edc_check sets the error-detecting algorithm. + * + * @param plist + * Identifier for the dataset transfer property list. + * @param check + * the error-detecting algorithm to use. + * + * @return non-negative if succeed + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public synchronized static native int H5Pset_edc_check(long plist, int check) throws HDF5LibraryException; /** * H5Pget_btree_ratio Get the B-tree split ratios for a dataset transfer property list. @@ -7524,9 +9579,46 @@ public class H5 implements java.io.Serializable { public synchronized static native int H5Pset_btree_ratios(long plist_id, double left, double middle, double right) throws HDF5LibraryException; + /** + * H5Pget_hyper_vector_size reads values previously set with H5Pset_hyper_vector_size. + * + * @param dxpl_id + * IN: Dataset transfer property list identifier. + * @param vector_size + * OUT: hyper vector size. + * + * @return a non-negative value if successful; otherwise returns a negative value. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * + **/ public synchronized static native int H5Pget_hyper_vector_size(long dxpl_id, long[] vector_size) throws HDF5LibraryException, NullPointerException; + /** + * H5Pset_hyper_vector_size sets the number of + * "I/O vectors" (offset and length pairs) which are to be + * accumulated in memory before being issued to the lower levels + * of the library for reading or writing the actual data. + * Increasing the number should give better performance, but use + * more memory during hyperslab I/O. The vector size must be + * greater than 1. + *,p. + * The default is to use 1024 vectors for I/O during hyperslab + * reading/writing. + * + * @param dxpl_id + * IN: Dataset transfer property list identifier. + * @param vector_size + * IN: hyper vestor size. + * + * @return a non-negative value if successful; otherwise returns a negative value. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * + **/ public synchronized static native int H5Pset_hyper_vector_size(long dxpl_id, long vector_size) throws HDF5LibraryException, NullPointerException; @@ -7724,8 +9816,32 @@ public class H5 implements java.io.Serializable { // /////// String creation property list (STRCPL) routines /////// + /** + * H5Pget_char_encoding gets the character encoding of the string. + * + * @param plist_id + * IN: the property list identifier + * + * @return Returns the character encoding of the string. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * + **/ public synchronized static native int H5Pget_char_encoding(long plist_id) throws HDF5LibraryException; + /** + * H5Pset_char_encoding sets the character encoding of the string. + * + * @param plist_id + * IN: the property list identifier + * @param encoding + * IN: the character encoding of the string + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * + **/ public synchronized static native void H5Pset_char_encoding(long plist_id, int encoding) throws HDF5LibraryException; @@ -7915,20 +10031,51 @@ public class H5 implements java.io.Serializable { // /////// file drivers property list routines /////// + /** + * H5Pget_fapl_core retrieve H5FD_CORE I/O settings. + * + * @param fapl_id + * IN: File access property list identifier + * @param increment + * OUT: how much to grow the memory each time + * @param backing_store + * OUT: write to file name on flush setting + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * + **/ public synchronized static native void H5Pget_fapl_core(long fapl_id, long[] increment, boolean[] backing_store) throws HDF5LibraryException, NullPointerException; + /** + * H5Pset_fapl_core modifies the file access property list to use the H5FD_CORE driver. + * + * @param fapl_id + * IN: File access property list identifier + * @param increment + * IN: how much to grow the memory each time + * @param backing_store + * IN: write to file name on flush setting + * + * @return a non-negative value if successful; otherwise returns a negative value. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * + **/ public synchronized static native int H5Pset_fapl_core(long fapl_id, long increment, boolean backing_store) throws HDF5LibraryException, NullPointerException; /** - * H5Pget_fapl_direct Retrieve direct I/O settings. + * H5Pget_fapl_direct queries properties set by the H5Pset_fapl_direct. * * @param fapl_id * IN: File access property list identifier * @param info - * OUT: Returned property list information info[0] = alignment Required memory alignment boundary info[1] - * = block_size File system block size info[2] = cbuf_size Copy buffer size + * OUT: Returned property list information + * info[0] = increment -how much to grow the memory each time + * info[1] = backing_store - write to file name on flush setting * * @return a non-negative value if successful; otherwise returns a negative value. * @@ -7959,14 +10106,72 @@ public class H5 implements java.io.Serializable { public synchronized static native int H5Pset_fapl_direct(long fapl_id, long alignment, long block_size, long cbuf_size) throws HDF5LibraryException; + /** + * H5Pget_fapl_family Returns information about the family file access property list. + * + * @param fapl_id + * IN: File access property list identifier + * @param memb_size + * OUT: the size in bytes of each file member (used only when creating a new file) + * @param memb_fapl_id + * OUT: the file access property list to be used for each family member + * + * @return a non-negative value if successful; otherwise returns a negative value. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * + **/ public synchronized static native int H5Pget_fapl_family(long fapl_id, long[] memb_size, long[] memb_fapl_id) throws HDF5LibraryException, NullPointerException; + /** + * H5Pset_fapl_family Sets up use of the direct I/O driver. + * + * @param fapl_id + * IN: File access property list identifier + * @param memb_size + * IN: the size in bytes of each file member (used only when creating a new file) + * @param memb_fapl_id + * IN: the file access property list to be used for each family member + * + * @return a non-negative value if successful; otherwise returns a negative value. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * + **/ public synchronized static native int H5Pset_fapl_family(long fapl_id, long memb_size, long memb_fapl_id) throws HDF5LibraryException, NullPointerException; + /** + * H5Pset_fapl_hdfs Modify the file access property list to use the H5FD_HDFS driver. + * + * @param fapl_id + * IN: File access property list identifier + * @param fapl_conf + * IN: the properties of the hdfs driver + * + * @return a non-negative value if successful; otherwise returns a negative value. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * + **/ public synchronized static native int H5Pset_fapl_hdfs(long fapl_id, H5FD_hdfs_fapl_t fapl_conf) throws HDF5LibraryException, NullPointerException; + /** + * H5Pget_fapl_hdfs gets the properties hdfs I/O driver. + * + * @param fapl_id + * IN: File access property list identifier + * + * @return the properties of the hdfs driver. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * + **/ public synchronized static native H5FD_hdfs_fapl_t H5Pget_fapl_hdfs(long fapl_id) throws HDF5LibraryException, NullPointerException; /** @@ -8044,17 +10249,99 @@ public class H5 implements java.io.Serializable { public synchronized static native void H5Pset_fapl_log(long fapl_id, String logfile, long flags, long buf_size) throws HDF5LibraryException, NullPointerException; + /** + * H5Pset_fapl_sec2 Sets up use of the sec2 I/O driver. + * + * @param fapl_id + * IN: File access property list identifier + * + * @return a non-negative value if successful; otherwise returns a negative value. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * + **/ public synchronized static native int H5Pset_fapl_sec2(long fapl_id) throws HDF5LibraryException, NullPointerException; + /** + * H5Pset_fapl_split Sets up use of the split I/O driver. Makes the multi driver act like the + * old split driver which stored meta data in one file and raw + * data in another file + * + * @param fapl_id + * IN: File access property list identifier + * @param meta_ext + * IN: meta filename extension + * @param meta_plist_id + * IN: File access property list identifier for metadata + * @param raw_ext + * IN: raw data filename extension + * @param raw_plist_id + * IN: File access property list identifier raw data + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * + **/ public synchronized static native void H5Pset_fapl_split(long fapl_id, String meta_ext, long meta_plist_id, String raw_ext, long raw_plist_id) throws HDF5LibraryException, NullPointerException; + /** + * H5Pset_fapl_stdio Sets up use of the stdio I/O driver. + * + * @param fapl_id + * IN: File access property list identifier + * + * @return a non-negative value if successful; otherwise returns a negative value. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * + **/ public synchronized static native int H5Pset_fapl_stdio(long fapl_id) throws HDF5LibraryException, NullPointerException; + /** + * H5Pset_fapl_windows Sets up use of the windows I/O driver. + * + * @param fapl_id + * IN: File access property list identifier + * + * @return a non-negative value if successful; otherwise returns a negative value. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * + **/ public synchronized static native int H5Pset_fapl_windows(long fapl_id) throws HDF5LibraryException, NullPointerException; + /** + * H5Pset_fapl_ros3 Modify the file access property list to use the H5FD_ROS3 driver. + * + * @param fapl_id + * IN: File access property list identifier + * @param fapl_conf + * IN: the properties of the ros3 driver + * + * @return a non-negative value if successful; otherwise returns a negative value. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * + **/ public synchronized static native int H5Pset_fapl_ros3(long fapl_id, H5FD_ros3_fapl_t fapl_conf) throws HDF5LibraryException, NullPointerException; + /** + * H5Pget_fapl_ros3 gets the properties of the ros3 I/O driver. + * + * @param fapl_id + * IN: File access property list identifier + * + * @return the properties of the ros3 driver. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * + **/ public synchronized static native H5FD_ros3_fapl_t H5Pget_fapl_ros3(long fapl_id) throws HDF5LibraryException, NullPointerException; // /////// unimplemented //////// @@ -8439,7 +10726,18 @@ public class H5 implements java.io.Serializable { * @exception IllegalArgumentException * - an input array is invalid. **/ - public synchronized static native long H5Ropen_object(byte[] ref_ptr, long rapl_id, long oapl_id) + public static long H5Ropen_object(byte[] ref_ptr, long rapl_id, long oapl_id) + throws HDF5LibraryException, NullPointerException, IllegalArgumentException { + long id = _H5Ropen_object(ref_ptr, rapl_id, oapl_id); + if (id > 0) { + log.trace("OPEN_IDS: H5Ropen_object add {}", id); + OPEN_IDS.add(id); + log.trace("OPEN_IDS: {}", OPEN_IDS.size()); + } + return id; + } + + private synchronized static native long _H5Ropen_object(byte[] ref_ptr, long rapl_id, long oapl_id) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** @@ -8467,7 +10765,18 @@ public class H5 implements java.io.Serializable { * @exception IllegalArgumentException * - an input array is invalid. **/ - public synchronized static native long H5Ropen_region(byte[] ref_ptr, long rapl_id, long oapl_id) + public static long H5Ropen_region(byte[] ref_ptr, long rapl_id, long oapl_id) + throws HDF5LibraryException, NullPointerException, IllegalArgumentException { + long id = _H5Ropen_region(ref_ptr, rapl_id, oapl_id); + if (id > 0) { + log.trace("OPEN_IDS: H5Ropen_region add {}", id); + OPEN_IDS.add(id); + log.trace("OPEN_IDS: {}", OPEN_IDS.size()); + } + return id; + } + + private synchronized static native long _H5Ropen_region(byte[] ref_ptr, long rapl_id, long oapl_id) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** @@ -8495,7 +10804,18 @@ public class H5 implements java.io.Serializable { * @exception IllegalArgumentException * - an input array is invalid. **/ - public synchronized static native long H5Ropen_attr(byte[] ref_ptr, long rapl_id, long aapl_id) + public static long H5Ropen_attr(byte[] ref_ptr, long rapl_id, long aapl_id) + throws HDF5LibraryException, NullPointerException, IllegalArgumentException { + long id = _H5Ropen_attr(ref_ptr, rapl_id, aapl_id); + if (id > 0) { + log.trace("OPEN_IDS: H5Ropen_attr add {}", id); + OPEN_IDS.add(id); + log.trace("OPEN_IDS: {}", OPEN_IDS.size()); + } + return id; + } + + private synchronized static native long _H5Ropen_attr(byte[] ref_ptr, long rapl_id, long aapl_id) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; // Get type // @@ -8762,50 +11082,7 @@ public class H5 implements java.io.Serializable { // // // //////////////////////////////////////////////////////////// - /** - * H5Sclose releases a dataspace. - * - * @param space_id - * Identifier of dataspace to release. - * - * @return a non-negative value if successful - * - * @exception HDF5LibraryException - * - Error from the HDF-5 Library. - **/ - public static int H5Sclose(long space_id) throws HDF5LibraryException { - if (space_id < 0) - return 0; // throw new HDF5LibraryException("Negative ID");; - - log.trace("OPEN_IDS: H5Sclose remove {}", space_id); - OPEN_IDS.remove(space_id); - log.trace("OPEN_IDS: {}", OPEN_IDS.size()); - return _H5Sclose(space_id); - } - - private synchronized static native int _H5Sclose(long space_id) throws HDF5LibraryException; - - /** - * H5Scopy creates a new dataspace which is an exact copy of the dataspace identified by space_id. - * - * @param space_id - * Identifier of dataspace to copy. - * @return a dataspace identifier if successful - * - * @exception HDF5LibraryException - * - Error from the HDF-5 Library. - **/ - public static long H5Scopy(long space_id) throws HDF5LibraryException { - long id = _H5Scopy(space_id); - if (id > 0) { - log.trace("OPEN_IDS: H5Scopy add {}", id); - OPEN_IDS.add(id); - log.trace("OPEN_IDS: {}", OPEN_IDS.size()); - } - return id; - } - - private synchronized static native long _H5Scopy(long space_id) throws HDF5LibraryException; + /**************** Operations on dataspaces ********************/ /** * H5Screate creates a new dataspace of a particular type. @@ -8862,19 +11139,96 @@ public class H5 implements java.io.Serializable { throws HDF5Exception, NullPointerException; /** - * H5Sdecode reconstructs the HDF5 data space object and returns a new object handle for it. + * H5Sset_extent_simple sets or resets the size of an existing dataspace. * - * @param buf - * IN: Buffer for the data space object to be decoded. + * @param space_id + * Dataspace identifier. + * @param rank + * Rank, or dimensionality, of the dataspace. + * @param current_size + * Array containing current size of dataspace. + * @param maximum_size + * Array containing maximum size of dataspace. * - * @return a new object handle + * @return a dataspace identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. - * @exception NullPointerException - * - buf is null. **/ - public synchronized static native long H5Sdecode(byte[] buf) throws HDF5LibraryException, NullPointerException; + public synchronized static native long H5Sset_extent_simple(long space_id, int rank, long[] current_size, + long[] maximum_size) throws HDF5LibraryException, NullPointerException; + + /** + * H5Sset_extent_simple sets or resets the size of an existing dataspace. + * + * @param space_id + * Dataspace identifier. + * @param rank + * Rank, or dimensionality, of the dataspace. + * @param current_size + * Array containing current size of dataspace. + * @param maximum_size + * Array containing maximum size of dataspace. + * + * @return a dataspace identifier if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public synchronized static long H5Sset_extent_simple(long space_id, int rank, byte[] current_size, + byte[] maximum_size) throws HDF5LibraryException, NullPointerException { + ByteBuffer csbb = ByteBuffer.wrap(current_size); + long[] lacs = (csbb.asLongBuffer()).array(); + ByteBuffer maxsbb = ByteBuffer.wrap(maximum_size); + long[] lamaxs = (maxsbb.asLongBuffer()).array(); + + return H5Sset_extent_simple(space_id, rank, lacs, lamaxs); + } + + /** + * H5Scopy creates a new dataspace which is an exact copy of the dataspace identified by space_id. + * + * @param space_id + * Identifier of dataspace to copy. + * @return a dataspace identifier if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public static long H5Scopy(long space_id) throws HDF5LibraryException { + long id = _H5Scopy(space_id); + if (id > 0) { + log.trace("OPEN_IDS: H5Scopy add {}", id); + OPEN_IDS.add(id); + log.trace("OPEN_IDS: {}", OPEN_IDS.size()); + } + return id; + } + + private synchronized static native long _H5Scopy(long space_id) throws HDF5LibraryException; + + /** + * H5Sclose releases a dataspace. + * + * @param space_id + * Identifier of dataspace to release. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public static int H5Sclose(long space_id) throws HDF5LibraryException { + if (space_id < 0) + return 0; // throw new HDF5LibraryException("Negative ID");; + + log.trace("OPEN_IDS: H5Sclose remove {}", space_id); + OPEN_IDS.remove(space_id); + log.trace("OPEN_IDS: {}", OPEN_IDS.size()); + return _H5Sclose(space_id); + } + + private synchronized static native int _H5Sclose(long space_id) throws HDF5LibraryException; /** * H5Sencode converts a data space description into binary form in a buffer. @@ -8890,154 +11244,139 @@ public class H5 implements java.io.Serializable { public synchronized static native byte[] H5Sencode(long obj_id) throws HDF5LibraryException, NullPointerException; /** - * H5Sextent_copy copies the extent from source_space_id to dest_space_id. This action may change the type of the - * dataspace. + * H5Sdecode reconstructs the HDF5 data space object and returns a new object handle for it. * - * @param dest_space_id - * IN: The identifier for the dataspace from which the extent is copied. - * @param source_space_id - * IN: The identifier for the dataspace to which the extent is copied. + * @param buf + * IN: Buffer for the data space object to be decoded. * - * @return a non-negative value if successful + * @return a new object handle * * @exception HDF5LibraryException * - Error from the HDF-5 Library. + * @exception NullPointerException + * - buf is null. **/ - public synchronized static native int H5Sextent_copy(long dest_space_id, long source_space_id) - throws HDF5LibraryException; + public synchronized static native long H5Sdecode(byte[] buf) throws HDF5LibraryException, NullPointerException; /** - * H5Sextent_equal determines whether the dataspace extents of two dataspaces, space1_id and space2_id, are equal. + * H5Sget_simple_extent_npoints determines the number of elements in a dataspace. * - * @param first_space_id - * IN: The identifier for the first dataspace. - * @param second_space_id - * IN: The identifier for the seconddataspace. + * @param space_id + * ID of the dataspace object to query + * @return the number of elements in the dataspace if successful * - * @return true if successful, else false + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public synchronized static native long H5Sget_simple_extent_npoints(long space_id) throws HDF5LibraryException; + + /** + * H5Sget_simple_extent_ndims determines the dimensionality (or rank) of a dataspace. + * + * @param space_id + * IN: Identifier of the dataspace + * + * @return the number of dimensions in the dataspace if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ - public synchronized static native boolean H5Sextent_equal(long first_space_id, long second_space_id) - throws HDF5LibraryException; + public synchronized static native int H5Sget_simple_extent_ndims(long space_id) throws HDF5LibraryException; /** - * H5Sget_select_bounds retrieves the coordinates of the bounding box containing the current selection and places - * them into user-supplied buffers. - * <P> - * The start and end buffers must be large enough to hold the dataspace rank number of coordinates. + * H5Sget_simple_extent_dims returns the size and maximum sizes of each dimension of a dataspace through the dims + * and maxdims parameters. * - * @param spaceid - * Identifier of dataspace to release. - * @param start - * coordinates of lowest corner of bounding box. - * @param end - * coordinates of highest corner of bounding box. + * @param space_id + * IN: Identifier of the dataspace object to query + * @param dims + * OUT: Pointer to array to store the size of each dimension. + * @param maxdims + * OUT: Pointer to array to store the maximum size of each dimension. * - * @return a non-negative value if successful,with start and end initialized. + * @return the number of dimensions in the dataspace if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException - * - start or end is null. + * - dims or maxdims is null. **/ - public synchronized static native int H5Sget_select_bounds(long spaceid, long[] start, long[] end) + public synchronized static native int H5Sget_simple_extent_dims(long space_id, long[] dims, long[] maxdims) throws HDF5LibraryException, NullPointerException; /** - * H5Sget_select_elem_npoints returns the number of element points in the current dataspace selection. + * H5Sis_simple determines whether a dataspace is a simple dataspace. * - * @param spaceid - * Identifier of dataspace to release. + * @param space_id + * Identifier of the dataspace to query * - * @return a non-negative value if successful + * @return true if is a simple dataspace * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ - public synchronized static native long H5Sget_select_elem_npoints(long spaceid) throws HDF5LibraryException; + public synchronized static native boolean H5Sis_simple(long space_id) throws HDF5LibraryException; /** - * H5Sget_select_elem_pointlist returns an array of of element points in the current dataspace selection. The point - * coordinates have the same dimensionality (rank) as the dataspace they are located within, one coordinate per - * point. + * H5Sget_simple_extent_type queries a dataspace to determine the current class of a dataspace. * - * @param spaceid - * Identifier of dataspace to release. - * @param startpoint - * first point to retrieve - * @param numpoints - * number of points to retrieve - * @param buf - * returns points startblock to startblock+num-1, each points is <i>rank</i> longs. + * @param space_id + * Dataspace identifier. * - * @return a non-negative value if successful + * @return a dataspace class name if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. - * @exception NullPointerException - * - buf is null. **/ - public synchronized static native int H5Sget_select_elem_pointlist(long spaceid, long startpoint, long numpoints, - long[] buf) throws HDF5LibraryException, NullPointerException; + public synchronized static native int H5Sget_simple_extent_type(long space_id) throws HDF5LibraryException; /** - * H5Sget_select_hyper_blocklist returns an array of hyperslab blocks. The block coordinates have the same - * dimensionality (rank) as the dataspace they are located within. The list of blocks is formatted as follows: - * - * <pre> - * <"start" coordinate>, immediately followed by - * <"opposite" corner coordinate>, followed by - * the next "start" and "opposite" coordinates, - * etc. - * until all of the selected blocks have been listed. - * </pre> + * H5Sset_extent_none removes the extent from a dataspace and sets the type to H5S_NONE. * - * @param spaceid - * Identifier of dataspace to release. - * @param startblock - * first block to retrieve - * @param numblocks - * number of blocks to retrieve - * @param buf - * returns blocks startblock to startblock+num-1, each block is <i>rank</i> * 2 (corners) longs. + * @param space_id + * The identifier for the dataspace from which the extent is to be removed. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. - * @exception NullPointerException - * - buf is null. **/ - public synchronized static native int H5Sget_select_hyper_blocklist(long spaceid, long startblock, long numblocks, - long[] buf) throws HDF5LibraryException, NullPointerException; + public synchronized static native int H5Sset_extent_none(long space_id) throws HDF5LibraryException; /** - * H5Sget_select_hyper_nblocks returns the number of hyperslab blocks in the current dataspace selection. + * H5Sextent_copy copies the extent from source_space_id to dest_space_id. This action may change the type of the + * dataspace. * - * @param spaceid - * Identifier of dataspace to release. + * @param dest_space_id + * IN: The identifier for the dataspace from which the extent is copied. + * @param source_space_id + * IN: The identifier for the dataspace to which the extent is copied. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ - public synchronized static native long H5Sget_select_hyper_nblocks(long spaceid) throws HDF5LibraryException; + public synchronized static native int H5Sextent_copy(long dest_space_id, long source_space_id) + throws HDF5LibraryException; /** - * H5Sget_select_npoints determines the number of elements in the current selection of a dataspace. + * H5Sextent_equal determines whether the dataspace extents of two dataspaces, space1_id and space2_id, are equal. * - * @param space_id - * IN: Identifier of the dataspace object to query + * @param first_space_id + * IN: The identifier for the first dataspace. + * @param second_space_id + * IN: The identifier for the seconddataspace. * - * @return the number of elements in the selection if successful + * @return true if successful, else false * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ - public synchronized static native long H5Sget_select_npoints(long space_id) throws HDF5LibraryException; + public synchronized static native boolean H5Sextent_equal(long first_space_id, long second_space_id) + throws HDF5LibraryException; + + /***************** Operations on dataspace selections *****************/ /** * H5Sget_select_type retrieves the type of selection currently defined for the dataspace space_id. @@ -9053,76 +11392,118 @@ public class H5 implements java.io.Serializable { public synchronized static native int H5Sget_select_type(long space_id) throws HDF5LibraryException; /** - * H5Sget_simple_extent_dims returns the size and maximum sizes of each dimension of a dataspace through the dims - * and maxdims parameters. + * H5Sget_select_npoints determines the number of elements in the current selection of a dataspace. * * @param space_id * IN: Identifier of the dataspace object to query - * @param dims - * OUT: Pointer to array to store the size of each dimension. - * @param maxdims - * OUT: Pointer to array to store the maximum size of each dimension. * - * @return the number of dimensions in the dataspace if successful + * @return the number of elements in the selection if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. - * @exception NullPointerException - * - dims or maxdims is null. **/ - public synchronized static native int H5Sget_simple_extent_dims(long space_id, long[] dims, long[] maxdims) - throws HDF5LibraryException, NullPointerException; + public synchronized static native long H5Sget_select_npoints(long space_id) throws HDF5LibraryException; /** - * H5Sget_simple_extent_ndims determines the dimensionality (or rank) of a dataspace. + * H5Sselect_copy copies all the selection information (including offset) from the source + * dataspace to the destination dataspace. + * @param dst_id ID of the destination dataspace + * @param src_id ID of the source dataspace + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public synchronized static native void H5Sselect_copy(long dst_id, long src_id) throws HDF5LibraryException; + + /** + * H5Sselect_valid verifies that the selection for the dataspace. * * @param space_id - * IN: Identifier of the dataspace + * The identifier for the dataspace in which the selection is being reset. * - * @return the number of dimensions in the dataspace if successful + * @return true if the selection is contained within the extent and FALSE if it is not or is an error. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ - public synchronized static native int H5Sget_simple_extent_ndims(long space_id) throws HDF5LibraryException; + public synchronized static native boolean H5Sselect_valid(long space_id) throws HDF5LibraryException; /** - * H5Sget_simple_extent_npoints determines the number of elements in a dataspace. + * H5Sselect_adjust moves a selection by subtracting an offset from it. * * @param space_id - * ID of the dataspace object to query - * @return the number of elements in the dataspace if successful + * ID of dataspace to adjust + * @param offset + * Offset to subtract * * @exception HDF5LibraryException * - Error from the HDF-5 Library. + * @exception NullPointerException + * - offset is null. **/ - public synchronized static native long H5Sget_simple_extent_npoints(long space_id) throws HDF5LibraryException; + public synchronized static native void H5Sselect_adjust(long space_id, long[][] offset) + throws HDF5LibraryException, NullPointerException; /** - * H5Sget_simple_extent_type queries a dataspace to determine the current class of a dataspace. + * H5Sget_select_bounds retrieves the coordinates of the bounding box containing the current selection and places + * them into user-supplied buffers. + * <P> + * The start and end buffers must be large enough to hold the dataspace rank number of coordinates. * * @param space_id - * Dataspace identifier. + * Identifier of dataspace to release. + * @param start + * coordinates of lowest corner of bounding box. + * @param end + * coordinates of highest corner of bounding box. * - * @return a dataspace class name if successful + * @return a non-negative value if successful,with start and end initialized. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. + * @exception NullPointerException + * - start or end is null. **/ - public synchronized static native int H5Sget_simple_extent_type(long space_id) throws HDF5LibraryException; + public synchronized static native int H5Sget_select_bounds(long space_id, long[] start, long[] end) + throws HDF5LibraryException, NullPointerException; /** - * H5Sis_simple determines whether a dataspace is a simple dataspace. + * H5Sselect_shape_same checks to see if the current selection in the dataspaces are the same + * dimensionality and shape. + * This is primarily used for reading the entire selection in one swoop. + * + * @param space1_id ID of 1st Dataspace pointer to compare + * @param space2_id ID of 2nd Dataspace pointer to compare + * + * @return true if the selection is the same dimensionality and shape; + * false otherwise + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public synchronized static native boolean H5Sselect_shape_same(long space1_id, long space2_id) throws HDF5LibraryException; + + /** + * H5Sselect_intersect_block checks to see if the current selection in the + * dataspace intersects with the block given. * * @param space_id - * Identifier of the dataspace to query + * ID of dataspace pointer to compare + * @param start + * Starting coordinate of block + * @param end + * Opposite ("ending") coordinate of block * - * @return true if is a simple dataspace + * @return a TRUE if the current selection in the dataspace intersects with the block given + * FALSE otherwise * * @exception HDF5LibraryException * - Error from the HDF-5 Library. + * @exception NullPointerException + * - offset is null. **/ - public synchronized static native boolean H5Sis_simple(long space_id) throws HDF5LibraryException; + public synchronized static native boolean H5Sselect_intersect_block(long space_id, long[] start, long[] end) + throws HDF5LibraryException, NullPointerException; /** * H5Soffset_simple sets the offset of a simple dataspace space_id. @@ -9142,6 +11523,21 @@ public class H5 implements java.io.Serializable { public synchronized static native int H5Soffset_simple(long space_id, byte[] offset) throws HDF5LibraryException, NullPointerException; + /** + * H5Soffset_simple sets the offset of a simple dataspace space_id. + * + * @param space_id + * IN: The identifier for the dataspace object to reset. + * @param offset + * IN: The offset at which to position the selection. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - offset array is null. + **/ public synchronized static int H5Soffset_simple(long space_id, long[] offset) throws HDF5Exception, NullPointerException { if (offset == null) { @@ -9172,6 +11568,18 @@ public class H5 implements java.io.Serializable { public synchronized static native int H5Sselect_all(long space_id) throws HDF5LibraryException; /** + * H5Sselect_none resets the selection region for the dataspace space_id to include no elements. + * + * @param space_id + * IN: The identifier of the dataspace to be reset. + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public synchronized static native int H5Sselect_none(long space_id) throws HDF5LibraryException; + + /** * H5Sselect_elements selects array elements to be included in the selection for the space_id dataspace. * * @param space_id @@ -9229,6 +11637,43 @@ public class H5 implements java.io.Serializable { } /** + * H5Sget_select_elem_npoints returns the number of element points in the current dataspace selection. + * + * @param spaceid + * Identifier of dataspace to release. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public synchronized static native long H5Sget_select_elem_npoints(long spaceid) throws HDF5LibraryException; + + /** + * H5Sget_select_elem_pointlist returns an array of of element points in the current dataspace selection. The point + * coordinates have the same dimensionality (rank) as the dataspace they are located within, one coordinate per + * point. + * + * @param spaceid + * Identifier of dataspace to release. + * @param startpoint + * first point to retrieve + * @param numpoints + * number of points to retrieve + * @param buf + * returns points startblock to startblock+num-1, each points is <i>rank</i> longs. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - buf is null. + **/ + public synchronized static native int H5Sget_select_elem_pointlist(long spaceid, long startpoint, long numpoints, + long[] buf) throws HDF5LibraryException, NullPointerException; + + /** * H5Sselect_hyperslab selects a hyperslab region to add to the current selected region for the dataspace specified * by space_id. The start, stride, count, and block arrays must be the same size as the rank of the dataspace. * @@ -9268,76 +11713,118 @@ public class H5 implements java.io.Serializable { return H5Sselect_hyperslab(space_id, op, lastart, lastride, lacount, lablock); } - public synchronized static native int H5Sselect_hyperslab(long space_id, int op, long[] start, long[] stride, - long[] count, long[] block) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; - /** - * H5Sselect_none resets the selection region for the dataspace space_id to include no elements. + * H5Sselect_hyperslab selects a hyperslab region to add to the current selected region for the dataspace specified + * by space_id. The start, stride, count, and block arrays must be the same size as the rank of the dataspace. * * @param space_id - * IN: The identifier of the dataspace to be reset. + * IN: Identifier of dataspace selection to modify + * @param op + * IN: Operation to perform on current selection. + * @param start + * IN: Offset of start of hyperslab + * @param stride + * IN: Hyperslab stride. + * @param count + * IN: Number of blocks included in hyperslab. + * @param block + * IN: Size of block in hyperslab. + * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. + * @exception NullPointerException + * - an input array is null. + * @exception IllegalArgumentException + * - an input array is invalid. **/ - public synchronized static native int H5Sselect_none(long space_id) throws HDF5LibraryException; + public synchronized static native int H5Sselect_hyperslab(long space_id, int op, long[] start, long[] stride, + long[] count, long[] block) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; + /** - * H5Sselect_valid verifies that the selection for the dataspace. + * H5Scombine_hyperslab combines a hyperslab selection with the current selection for a dataspace, + * creating a new dataspace to return the generated selection. + * If the current selection is not a hyperslab, it is freed and the hyperslab + * parameters passed in are combined with the H5S_SEL_ALL hyperslab (ie. a + * selection composing the entire current extent). If STRIDE or BLOCK is + * NULL, they are assumed to be set to all '1'. * * @param space_id - * The identifier for the dataspace in which the selection is being reset. + * IN: Dataspace ID of selection to use + * @param op + * IN: Operation to perform on current selection. + * @param start + * IN: Offset of start of hyperslab + * @param stride + * IN: Hyperslab stride. + * @param count + * IN: Number of blocks included in hyperslab. + * @param block + * IN: Size of block in hyperslab. * - * @return true if the selection is contained within the extent and FALSE if it is not or is an error. + * @return a dataspace ID on success / H5I_INVALID_HID on failure * * @exception HDF5LibraryException * - Error from the HDF-5 Library. + * @exception NullPointerException + * - an input array is null. + * @exception IllegalArgumentException + * - an input array is invalid. **/ - public synchronized static native boolean H5Sselect_valid(long space_id) throws HDF5LibraryException; + public synchronized static native long H5Scombine_hyperslab(long space_id, int op, long[] start, long[] stride, + long[] count, long[] block) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** - * H5Sset_extent_none removes the extent from a dataspace and sets the type to H5S_NONE. + * H5Smodify_select refine an existing hyperslab selection with an operation, using a second + * hyperslab. The first selection is modified to contain the result of + * space1 operated on by space2. * - * @param space_id - * The identifier for the dataspace from which the extent is to be removed. + * @param space1_id + * ID of the destination dataspace + * @param op + * Operation to perform on current selection. + * @param space2_id + * ID of the source dataspace * - * @return a non-negative value if successful + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public synchronized static native void H5Smodify_select(long space1_id, int op, long space2_id) throws HDF5LibraryException; + + /** + * H5Scombine_select combines two existing hyperslab selections with an operation, returning + * a new dataspace with the resulting selection. The dataspace extent from + * space1 is copied for the dataspace extent of the newly created dataspace. + * + * @param space1_id + * ID of the first dataspace + * @param op + * Operation to perform on current selection. + * @param space2_id + * ID of the second dataspace + * + * @return a dataspace ID on success / H5I_INVALID_HID on failure * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ - public synchronized static native int H5Sset_extent_none(long space_id) throws HDF5LibraryException; + public synchronized static native long H5Scombine_select(long space1_id, int op, long space2_id) throws HDF5LibraryException; /** - * H5Sset_extent_simple sets or resets the size of an existing dataspace. + * H5Sis_regular_hyperslab retrieves a regular hyperslab selection for the dataspace specified + * by space_id. * * @param space_id - * Dataspace identifier. - * @param rank - * Rank, or dimensionality, of the dataspace. - * @param current_size - * Array containing current size of dataspace. - * @param maximum_size - * Array containing maximum size of dataspace. + * IN: Identifier of dataspace selection to query * - * @return a dataspace identifier if successful + * @return a TRUE/FALSE for hyperslab selection if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ - public synchronized static native long H5Sset_extent_simple(long space_id, int rank, long[] current_size, - long[] maximum_size) throws HDF5LibraryException, NullPointerException; - - public synchronized static long H5Sset_extent_simple(long space_id, int rank, byte[] current_size, - byte[] maximum_size) throws HDF5LibraryException, NullPointerException { - ByteBuffer csbb = ByteBuffer.wrap(current_size); - long[] lacs = (csbb.asLongBuffer()).array(); - ByteBuffer maxsbb = ByteBuffer.wrap(maximum_size); - long[] lamaxs = (maxsbb.asLongBuffer()).array(); - - return H5Sset_extent_simple(space_id, rank, lacs, lamaxs); - } + public synchronized static native boolean H5Sis_regular_hyperslab(long space_id) throws HDF5LibraryException; /** * H5Sget_regular_hyperslab determines if a hyperslab selection is regular for the dataspace specified @@ -9363,33 +11850,82 @@ public class H5 implements java.io.Serializable { **/ public synchronized static native void H5Sget_regular_hyperslab(long space_id, long[] start, long[] stride, long[] count, long[] block) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; + /** + * H5Sget_select_hyper_nblocks returns the number of hyperslab blocks in the current dataspace selection. + * + * @param spaceid + * Identifier of dataspace to release. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public synchronized static native long H5Sget_select_hyper_nblocks(long spaceid) throws HDF5LibraryException; + /** - * H5Sis_regular_hyperslab retrieves a regular hyperslab selection for the dataspace specified - * by space_id. + * H5Sget_select_hyper_blocklist returns an array of hyperslab blocks. The block coordinates have the same + * dimensionality (rank) as the dataspace they are located within. The list of blocks is formatted as follows: * - * @param space_id - * IN: Identifier of dataspace selection to query + * <pre> + * <"start" coordinate>, immediately followed by + * <"opposite" corner coordinate>, followed by + * the next "start" and "opposite" coordinates, + * etc. + * until all of the selected blocks have been listed. + * </pre> * - * @return a TRUE/FALSE for hyperslab selection if successful + * @param spaceid + * Identifier of dataspace to release. + * @param startblock + * first block to retrieve + * @param numblocks + * number of blocks to retrieve + * @param buf + * returns blocks startblock to startblock+num-1, each block is <i>rank</i> * 2 (corners) longs. + * + * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. + * @exception NullPointerException + * - buf is null. **/ - public synchronized static native boolean H5Sis_regular_hyperslab(long space_id) throws HDF5LibraryException; + public synchronized static native int H5Sget_select_hyper_blocklist(long spaceid, long startblock, long numblocks, + long[] buf) throws HDF5LibraryException, NullPointerException; - // /////// unimplemented //////// - // #ifdef NEW_HYPERSLAB_API - // hid_t H5Scombine_hyperslab(hid_t space_id, H5S_seloper_t op, - // const hsize_t start[], - // const hsize_t _stride[], - // const hsize_t count[], - // const hsize_t _block[]); - // herr_t H5Sselect_select(hid_t space1_id, H5S_seloper_t op, - // hid_t space2_id); - // hid_t H5Scombine_select(hid_t space1_id, H5S_seloper_t op, - // hid_t space2_id); - // #endif /* NEW_HYPERSLAB_API */ - // herr_t H5Sselect_copy(hid_t dst_id, hid_t src_id); + /** + * H5Sselect_project_intersection projects the intersection of the selections of src_space_id and + * src_intersect_space_id within the selection of src_space_id as a + * selection within the selection of dst_space_id. + * + * @param src_space_id + * Selection that is mapped to dst_space_id, and intersected with src_intersect_space_id + * @param dst_space_id + * Selection that is mapped to src_space_id + * @param src_intersect_space_id + * Selection whose intersection with src_space_id is projected to dst_space_id to obtain the result + * + * @return a dataspace with a selection equal to the intersection of + * src_intersect_space_id and src_space_id projected from src_space to dst_space on success + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public synchronized static native long H5Sselect_project_intersection(long src_space_id, long dst_space_id, + long src_intersect_space_id) throws HDF5LibraryException; + + + // /////// unimplemented //////// + ///// Operations on dataspace selections ///// + + // + ///// Operations on dataspace selection iterators ///// + //public synchronized static native H5Ssel_iter_create(hid_t spaceid, size_t elmt_size, unsigned flags); + //public synchronized static native H5Ssel_iter_get_seq_list(hid_t sel_iter_id, size_t maxseq, size_t maxbytes, size_t *nseq, + // size_t *nbytes, hsize_t *off, size_t *len); + //public synchronized static native H5Ssel_iter_reset(hid_t sel_iter_id, hid_t space_id); + //public synchronized static native H5Ssel_iter_close(hid_t sel_iter_id); @@ -9737,6 +12273,23 @@ public class H5 implements java.io.Serializable { return H5Tenum_insert_int(type, name, value); } + /** + * H5Tenum_insert inserts a new enumeration datatype member into an enumeration datatype. + * + * @param type + * IN: Identifier of datatype. + * @param name + * IN: The name of the member + * @param value + * IN: The value of the member, data of the correct type + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ public static int H5Tenum_insert(long type, String name, int value) throws HDF5LibraryException, NullPointerException { int[] val = { value }; @@ -10893,15 +13446,128 @@ public class H5 implements java.io.Serializable { // //////////////////////////////////////////////////////////// /// VOL Connector Functionality + /** + * H5VLregister_connector_by_name registers a new VOL connector as a member of the virtual object layer class. + * + * @param connector_name + * IN: name of the connector. + * @param vipl_id + * IN: VOL initialization property list which must be + * created with H5Pcreate(H5P_VOL_INITIALIZE) (or H5P_DEFAULT). + * + * @return a VOL connector ID + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native long H5VLregister_connector_by_name(String connector_name, long vipl_id); + /** + * H5VLregister_connector_by_value registers a new VOL connector as a member of the virtual object layer class. + * + * @param connector_value + * IN: value of the connector. + * @param vipl_id + * IN: VOL initialization property list which must be + * created with H5Pcreate(H5P_VOL_INITIALIZE) (or H5P_DEFAULT). + * + * @return a VOL connector ID + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native long H5VLregister_connector_by_value(int connector_value, long vipl_id); + /** + * H5VLis_connector_registered_by_name tests whether a VOL class has been registered. + * + * @param name + * IN: name of the connector. + * + * @return true if a VOL connector with that name has been registered + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native boolean H5VLis_connector_registered_by_name(String name); + /** + * H5VLis_connector_registered_by_value tests whether a VOL class has been registered. + * + * @param connector_value + * IN: value of the connector. + * + * @return true if a VOL connector with that value has been registered + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native boolean H5VLis_connector_registered_by_value(int connector_value); + /** + * H5VLget_connector_id retrieves the ID for a registered VOL connector for a given object. + * + * @param object_id + * IN: Identifier of the object. + * + * @return a VOL connector ID + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native long H5VLget_connector_id(long object_id); + /** + * H5VLget_connector_id_by_name retrieves the ID for a registered VOL connector. + * + * @param name + * IN: name of the connector. + * + * @return a VOL connector ID + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native long H5VLget_connector_id_by_name(String name); + /** + * H5VLget_connector_id_by_value retrieves the ID for a registered VOL connector. + * + * @param connector_value + * IN: value of the connector. + * + * @return a VOL connector ID + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native long H5VLget_connector_id_by_value(int connector_value); + /** + * H5VLget_connector_name returns the connector name for the VOL associated with the + * object or file ID. + * + * @param object_id + * IN: Identifier of the object. + * + * @return the connector name + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native String H5VLget_connector_name(long object_id); + /** + * H5VLclose closes a VOL connector ID. + * + * @param connector_id + * IN: Identifier of the connector. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native void H5VLclose(long connector_id); + /** + * H5VLunregister_connector removes a VOL connector ID from the library. + * + * @param connector_id + * IN: Identifier of the connector. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native void H5VLunregister_connector(long connector_id); // /////// unimplemented //////// @@ -10914,11 +13580,44 @@ public class H5 implements java.io.Serializable { // // // //////////////////////////////////////////////////////////// - public synchronized static native int H5Zfilter_avail(int filter) throws HDF5LibraryException, NullPointerException; + /** + * H5Zfilter_avail checks if a filter is available. + * + * @param filter + * IN: filter number. + * + * @return a non-negative(TRUE/FALSE) value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public synchronized static native int H5Zfilter_avail(int filter) throws HDF5LibraryException; + /** + * H5Zget_filter_info gets information about a pipeline data filter. + * + * @param filter + * IN: filter number. + * + * @return the filter information flags + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ public synchronized static native int H5Zget_filter_info(int filter) throws HDF5LibraryException; - public synchronized static native int H5Zunregister(int filter) throws HDF5LibraryException, NullPointerException; + /** + * H5Zunregister unregisters a filter. + * + * @param filter + * IN: filter number. + * + * @return a non-negative value if successful + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + **/ + public synchronized static native int H5Zunregister(int filter) throws HDF5LibraryException; // /////// unimplemented //////// diff --git a/java/src/hdf/hdf5lib/HDF5Constants.java b/java/src/hdf/hdf5lib/HDF5Constants.java index b390183..153bc71 100644 --- a/java/src/hdf/hdf5lib/HDF5Constants.java +++ b/java/src/hdf/hdf5lib/HDF5Constants.java @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -35,21 +35,35 @@ public class HDF5Constants { // Get the HDF5 constants from the library // // ///////////////////////////////////////////////////////////////////////// - public static final long H5_QUARTER_HADDR_MAX = H5_QUARTER_HADDR_MAX(); + //public static final long H5_QUARTER_HADDR_MAX = H5_QUARTER_HADDR_MAX(); + /** Special parameters for szip compression */ public static final int H5_SZIP_MAX_PIXELS_PER_BLOCK = H5_SZIP_MAX_PIXELS_PER_BLOCK(); + /** Special parameters for szip compression */ public static final int H5_SZIP_NN_OPTION_MASK = H5_SZIP_NN_OPTION_MASK(); + /** Special parameters for szip compression */ public static final int H5_SZIP_EC_OPTION_MASK = H5_SZIP_EC_OPTION_MASK(); + /** Special parameters for szip compression */ public static final int H5_SZIP_ALLOW_K13_OPTION_MASK = H5_SZIP_ALLOW_K13_OPTION_MASK(); + /** Special parameters for szip compression */ public static final int H5_SZIP_CHIP_OPTION_MASK = H5_SZIP_CHIP_OPTION_MASK(); + /** indices on links, unknown index type */ public static final int H5_INDEX_UNKNOWN = H5_INDEX_UNKNOWN(); + /** indices on links, index on names */ public static final int H5_INDEX_NAME = H5_INDEX_NAME(); + /** indices on links, index on creation order */ public static final int H5_INDEX_CRT_ORDER = H5_INDEX_CRT_ORDER(); + /** indices on links, number of indices defined */ public static final int H5_INDEX_N = H5_INDEX_N(); + /** Common iteration orders, Unknown order */ public static final int H5_ITER_UNKNOWN = H5_ITER_UNKNOWN(); + /** Common iteration orders, Increasing order */ public static final int H5_ITER_INC = H5_ITER_INC(); + /** Common iteration orders, Decreasing order */ public static final int H5_ITER_DEC = H5_ITER_DEC(); + /** Common iteration orders, No particular order, whatever is fastest */ public static final int H5_ITER_NATIVE = H5_ITER_NATIVE(); + /** Common iteration orders, Number of iteration orders */ public static final int H5_ITER_N = H5_ITER_N(); public static final int H5AC_CURR_CACHE_CONFIG_VERSION = H5AC_CURR_CACHE_CONFIG_VERSION(); public static final int H5AC_MAX_TRACE_FILE_NAME_LEN = H5AC_MAX_TRACE_FILE_NAME_LEN(); @@ -92,110 +106,359 @@ public class HDF5Constants { public static final int H5D_VDS_LAST_AVAILABLE = H5D_VDS_LAST_AVAILABLE(); public static final int H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS = H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS(); + /** Different kinds of error information - H5E_type_t */ public static final int H5E_MAJOR = H5E_MAJOR(); + /** Different kinds of error information - H5E_type_t */ public static final int H5E_MINOR = H5E_MINOR(); + /** Minor error codes - Object header related errors - Alignment error */ public static final long H5E_ALIGNMENT = H5E_ALIGNMENT(); + /** Minor error codes - Resource errors - Object already exists */ public static final long H5E_ALREADYEXISTS = H5E_ALREADYEXISTS(); + /** Minor error codes - Function entry/exit interface - Object already initialized */ public static final long H5E_ALREADYINIT = H5E_ALREADYINIT(); + /** Major error codes - Invalid arguments to routine */ public static final long H5E_ARGS = H5E_ARGS(); + /** Major error codes - Object atom */ public static final long H5E_ATOM = H5E_ATOM(); + /** Major error codes - Attribute */ public static final long H5E_ATTR = H5E_ATTR(); + /** Minor error codes - Object atom related errors - Unable to find atom information (already closed?) */ public static final long H5E_BADATOM = H5E_BADATOM(); + /** Minor error codes - File accessibility errors - Bad file ID accessed */ public static final long H5E_BADFILE = H5E_BADFILE(); + /** Minor error codes - Object atom related errors - Unable to find ID group information */ public static final long H5E_BADGROUP = H5E_BADGROUP(); + /** Minor error codes - Object header related errors - Iteration failed */ + public static final long H5E_BADITER = H5E_BADITER(); + /** Minor error codes - Object header related errors - Unrecognized message */ public static final long H5E_BADMESG = H5E_BADMESG(); + /** Minor error codes - Argument errors - Out of range */ public static final long H5E_BADRANGE = H5E_BADRANGE(); + /** Minor error codes - Dataspace errors - Invalid selection */ public static final long H5E_BADSELECT = H5E_BADSELECT(); + /** Datatype conversion errors - Bad size for object */ public static final long H5E_BADSIZE = H5E_BADSIZE(); + /** Minor error codes - Argument errors - Inappropriate type */ public static final long H5E_BADTYPE = H5E_BADTYPE(); + /** Minor error codes - Argument errors - Bad value */ public static final long H5E_BADVALUE = H5E_BADVALUE(); + /** Major error codes - B-Tree node */ public static final long H5E_BTREE = H5E_BTREE(); + /** Major error codes - Object cache */ public static final long H5E_CACHE = H5E_CACHE(); + /** I/O pipeline errors - Callback failed */ public static final long H5E_CALLBACK = H5E_CALLBACK(); + /** I/O pipeline errors - Error from filter 'can apply' callback */ public static final long H5E_CANAPPLY = H5E_CANAPPLY(); - // public static final long H5E_CANTALLOC = H5E_CANTALLOC(); + /** Minor error codes - Resource errors - Can't allocate space */ + public static final long H5E_CANTALLOC = H5E_CANTALLOC(); + /** Minor error codes - Dataspace errors - Can't append object */ + public static final long H5E_CANTAPPEND = H5E_CANTAPPEND(); + /** Minor error codes - Heap errors - Can't attach object */ + public static final long H5E_CANTATTACH = H5E_CANTATTACH(); + /** Minor error codes - Cache related errors - Unable to mark metadata as clean */ + public static final long H5E_CANTCLEAN = H5E_CANTCLEAN(); + /** Minor error codes - Dataspace errors - Can't clip hyperslab region */ public static final long H5E_CANTCLIP = H5E_CANTCLIP(); + /** Minor error codes - File accessibility errors - Unable to close file */ public static final long H5E_CANTCLOSEFILE = H5E_CANTCLOSEFILE(); + /** Minor error codes - Group related errors - Can't close object */ + public static final long H5E_CANTCLOSEOBJ = H5E_CANTCLOSEOBJ(); + /** Minor error codes - Dataspace errors - Can't compare objects */ + public static final long H5E_CANTCOMPARE = H5E_CANTCOMPARE(); + /** Minor error codes - Heap errors - Can't compute value */ + public static final long H5E_CANTCOMPUTE = H5E_CANTCOMPUTE(); + /** Datatype conversion errors - Can't convert datatypes */ public static final long H5E_CANTCONVERT = H5E_CANTCONVERT(); + /** Minor error codes - Resource errors - Unable to copy object */ public static final long H5E_CANTCOPY = H5E_CANTCOPY(); + /** Minor error codes - Cache related errors - Unable to cork an object */ + public static final long H5E_CANTCORK = H5E_CANTCORK(); + /** Minor error codes - Dataspace errors - Can't count elements */ public static final long H5E_CANTCOUNT = H5E_CANTCOUNT(); + /** Minor error codes - File accessibility errors - Unable to create file */ public static final long H5E_CANTCREATE = H5E_CANTCREATE(); + /** Minor error codes - Object atom related errors - Unable to decrement reference count */ public static final long H5E_CANTDEC = H5E_CANTDEC(); + /** Minor error codes - B-tree related errors - Unable to decode value */ public static final long H5E_CANTDECODE = H5E_CANTDECODE(); + /** Minor error codes - Object header related errors - Can't delete message */ public static final long H5E_CANTDELETE = H5E_CANTDELETE(); + /** Minor error codes - File accessibility errors - Unable to delete file */ public static final long H5E_CANTDELETEFILE = H5E_CANTDELETEFILE(); + /** Minor error codes - Cache related errors - Unable to create a flush dependency */ + public static final long H5E_CANTDEPEND = H5E_CANTDEPEND(); + /** Minor error codes - Cache related errors - Unable to mark metadata as dirty */ + public static final long H5E_CANTDIRTY = H5E_CANTDIRTY(); + /** Minor error codes - B-tree related errors - Unable to encode value */ public static final long H5E_CANTENCODE = H5E_CANTENCODE(); + /** Minor error codes - Cache related errors - Unable to expunge a metadata cache entry */ + public static final long H5E_CANTEXPUNGE = H5E_CANTEXPUNGE(); + /** Minor error codes - Heap errors - Can't extend heap's space */ + public static final long H5E_CANTEXTEND = H5E_CANTEXTEND(); + /** I/O pipeline errors - Filter operation failed */ + public static final long H5E_CANTFILTER = H5E_CANTFILTER(); + /** Minor error codes - Cache related errors - Unable to flush data from cache */ public static final long H5E_CANTFLUSH = H5E_CANTFLUSH(); + /** Minor error codes - Resource errors - Unable to free object */ public static final long H5E_CANTFREE = H5E_CANTFREE(); + /** Minor error codes - Parallel MPI - Can't gather data */ + public static final long H5E_CANTGATHER = H5E_CANTGATHER(); + /** Minor error codes - Resource errors - Unable to garbage collect */ + public static final long H5E_CANTGC = H5E_CANTGC(); + /** Minor error codes - Property list errors - Can't get value */ public static final long H5E_CANTGET = H5E_CANTGET(); + /** Minor error codes - Resource errors - Unable to compute size */ + public static final long H5E_CANTGETSIZE = H5E_CANTGETSIZE(); + /** Minor error codes - Object atom related errors - Unable to increment reference count */ public static final long H5E_CANTINC = H5E_CANTINC(); + /** Minor error codes - Function entry/exit interface - Unable to initialize object */ public static final long H5E_CANTINIT = H5E_CANTINIT(); + /** Minor error codes - Cache related errors - Unable to insert metadata into cache */ + public static final long H5E_CANTINS = H5E_CANTINS(); + /** Minor error codes - B-tree related errors - Unable to insert object */ public static final long H5E_CANTINSERT = H5E_CANTINSERT(); + /** Minor error codes - B-tree related errors - Unable to list node */ public static final long H5E_CANTLIST = H5E_CANTLIST(); + /** Minor error codes - Cache related errors - Unable to load metadata into cache */ public static final long H5E_CANTLOAD = H5E_CANTLOAD(); + /** Minor error codes - Resource errors - Unable to lock object */ public static final long H5E_CANTLOCK = H5E_CANTLOCK(); + /** Minor error codes - File accessibility errors Unable to lock file */ + public static final long H5E_CANTLOCKFILE = H5E_CANTLOCKFILE(); + /** Minor error codes - Cache related errors - Unable to mark a pinned entry as clean */ + public static final long H5E_CANTMARKCLEAN = H5E_CANTMARKCLEAN(); + /** Minor error codes - Cache related errors - Unable to mark a pinned entry as dirty */ + public static final long H5E_CANTMARKDIRTY = H5E_CANTMARKDIRTY(); + /** Minor error codes - Cache related errors - Unable to mark an entry as unserialized */ + public static final long H5E_CANTMARKSERIALIZED = H5E_CANTMARKSERIALIZED(); + /** Minor error codes - Cache related errors - Unable to mark an entry as serialized */ + public static final long H5E_CANTMARKUNSERIALIZED = H5E_CANTMARKUNSERIALIZED(); + /** Minor error codes - Free space errors - Can't merge objects */ + public static final long H5E_CANTMERGE = H5E_CANTMERGE(); + /** Minor error codes - B-tree related errors - Unable to modify record */ + public static final long H5E_CANTMODIFY = H5E_CANTMODIFY(); + /** Minor error codes - Link related errors - Can't move object */ + public static final long H5E_CANTMOVE = H5E_CANTMOVE(); + /** Minor error codes - Dataspace errors - Can't move to next iterator location */ public static final long H5E_CANTNEXT = H5E_CANTNEXT(); + /** Minor error codes - Cache related errors - Unable to notify object about action */ + public static final long H5E_CANTNOTIFY = H5E_CANTNOTIFY(); + /** Minor error codes - File accessibility errors - Unable to open file */ public static final long H5E_CANTOPENFILE = H5E_CANTOPENFILE(); + /** Minor error codes - Group related errors - Can't open object */ public static final long H5E_CANTOPENOBJ = H5E_CANTOPENOBJ(); - // public static final long H5E_CANTRECV = H5E_CANTRECV(); + /** Minor error codes - Heap errors - Can't operate on object */ + public static final long H5E_CANTOPERATE = H5E_CANTOPERATE(); + /** Minor error codes - Object header related errors - Can't pack messages */ + public static final long H5E_CANTPACK = H5E_CANTPACK(); + /** Minor error codes - Cache related errors - Unable to pin cache entry */ + public static final long H5E_CANTPIN = H5E_CANTPIN(); + /** Minor error codes - Cache related errors - Unable to protect metadata */ + public static final long H5E_CANTPROTECT = H5E_CANTPROTECT(); + /** Minor error codes - Parallel MPI - Can't receive data */ + public static final long H5E_CANTRECV = H5E_CANTRECV(); + /** Minor error codes - B-tree related errors - Unable to redistribute records */ + public static final long H5E_CANTREDISTRIBUTE = H5E_CANTREDISTRIBUTE(); + /** Minor error codes - Object atom related errors - Unable to register new atom */ public static final long H5E_CANTREGISTER = H5E_CANTREGISTER(); + /** Minor error codes - Function entry/exit interface - Unable to release object */ public static final long H5E_CANTRELEASE = H5E_CANTRELEASE(); + /** Minor error codes - B-tree related errors - Unable to remove object */ + public static final long H5E_CANTREMOVE = H5E_CANTREMOVE(); + /** Minor error codes - Object header related errors - Unable to rename object */ + public static final long H5E_CANTRENAME = H5E_CANTRENAME(); + /** Minor error codes - Object header related errors - Can't reset object */ + public static final long H5E_CANTRESET = H5E_CANTRESET(); + /** Minor error codes - Cache related errors - Unable to resize a metadata cache entry */ + public static final long H5E_CANTRESIZE = H5E_CANTRESIZE(); + /** Minor error codes - Heap errors - Can't restore condition */ + public static final long H5E_CANTRESTORE = H5E_CANTRESTORE(); + /** Minor error codes - Free space errors - Can't revive object */ + public static final long H5E_CANTREVIVE = H5E_CANTREVIVE(); + /** Minor error codes - Free space errors - Can't shrink container */ + public static final long H5E_CANTSHRINK = H5E_CANTSHRINK(); + /** Minor error codes - Dataspace errors - Can't select hyperslab */ public static final long H5E_CANTSELECT = H5E_CANTSELECT(); + /** Minor error codes - Cache related errors - Unable to serialize data from cache */ + public static final long H5E_CANTSERIALIZE = H5E_CANTSERIALIZE(); + /** Minor error codes - Property list errors - Can't set value */ public static final long H5E_CANTSET = H5E_CANTSET(); + /** Minor error codes - Link related errors - Can't sort objects */ + public static final long H5E_CANTSORT = H5E_CANTSORT(); + /** Minor error codes - B-tree related errors - Unable to split node */ public static final long H5E_CANTSPLIT = H5E_CANTSPLIT(); + /** Minor error codes - B-tree related errors - Unable to swap records */ + public static final long H5E_CANTSWAP = H5E_CANTSWAP(); + /** Minor error codes - Cache related errors - Unable to tag metadata in the cache */ + public static final long H5E_CANTTAG = H5E_CANTTAG(); + /** Minor error codes - Cache related errors - Unable to uncork an object */ + public static final long H5E_CANTUNCORK = H5E_CANTUNCORK(); + /** Minor error codes - Cache related errors - Unable to destroy a flush dependency */ + public static final long H5E_CANTUNDEPEND = H5E_CANTUNDEPEND(); + /** Minor error codes - Resource errors - Unable to unlock object */ public static final long H5E_CANTUNLOCK = H5E_CANTUNLOCK(); + /** Minor error codes - File accessibility errors Unable to unlock file */ + public static final long H5E_CANTUNLOCKFILE = H5E_CANTUNLOCKFILE(); + /** Minor error codes - Cache related errors - Unable to un-pin cache entry */ + public static final long H5E_CANTUNPIN = H5E_CANTUNPIN(); + /** Minor error codes - Cache related errors - Unable to unprotect metadata */ + public static final long H5E_CANTUNPROTECT = H5E_CANTUNPROTECT(); + /** Minor error codes - Cache related errors - Unable to mark metadata as unserialized */ + public static final long H5E_CANTUNSERIALIZE = H5E_CANTUNSERIALIZE(); + /** Minor error codes - Heap errors - Can't update object */ + public static final long H5E_CANTUPDATE = H5E_CANTUPDATE(); + /** Generic low-level file I/O errors - Close failed */ public static final long H5E_CLOSEERROR = H5E_CLOSEERROR(); + /** Minor error codes - Group related errors - Name component is too long */ public static final long H5E_COMPLEN = H5E_COMPLEN(); + /** Major error codes - API Context */ + public static final long H5E_CONTEXT = H5E_CONTEXT(); + /** Major error codes - Dataset */ public static final long H5E_DATASET = H5E_DATASET(); + /** Major error codes - Dataspace */ public static final long H5E_DATASPACE = H5E_DATASPACE(); + /** Major error codes - Datatype */ public static final long H5E_DATATYPE = H5E_DATATYPE(); + /** Value for the default error stack */ public static final long H5E_DEFAULT = H5E_DEFAULT(); + /** Minor error codes - Property list errors - Duplicate class name in parent class */ public static final long H5E_DUPCLASS = H5E_DUPCLASS(); + /** Major error codes - Extensible Array */ + public static final long H5E_EARRAY = H5E_EARRAY(); + /** Major error codes - External file list */ public static final long H5E_EFL = H5E_EFL(); + /** Major error codes - Error API */ + public static final long H5E_ERROR = H5E_ERROR(); + /** Minor error codes - B-tree related errors - Object already exists */ public static final long H5E_EXISTS = H5E_EXISTS(); + /** Major error codes - Fixed Array */ + public static final long H5E_FARRAY = H5E_FARRAY(); + /** Generic low-level file I/O errors - File control (fcntl) failed */ public static final long H5E_FCNTL = H5E_FCNTL(); + /** Major error codes - File accessibility */ public static final long H5E_FILE = H5E_FILE(); + /** Minor error codes - File accessibility errors - File already exists */ public static final long H5E_FILEEXISTS = H5E_FILEEXISTS(); + /** Minor error codes - File accessibility errors - File already open */ public static final long H5E_FILEOPEN = H5E_FILEOPEN(); + /** Major error codes - Free Space Manager */ + public static final long H5E_FSPACE = H5E_FSPACE(); + /** Major error codes - Function entry/exit */ public static final long H5E_FUNC = H5E_FUNC(); + /** Major error codes - Heap */ public static final long H5E_HEAP = H5E_HEAP(); + /** Minor error codes - Dataspace errors - Internal states are inconsistent */ + public static final long H5E_INCONSISTENTSTATE = H5E_INCONSISTENTSTATE(); + /** Major error codes - Internal error (too specific to document in detail) */ public static final long H5E_INTERNAL = H5E_INTERNAL(); + /** Major error codes - Low-level I/O */ public static final long H5E_IO = H5E_IO(); + /** Major error codes - Links */ public static final long H5E_LINK = H5E_LINK(); + /** Minor error codes - Object header related errors - Bad object header link count */ public static final long H5E_LINKCOUNT = H5E_LINKCOUNT(); + /** Minor error codes - Cache related errors - Failure in the cache logging framework */ + public static final long H5E_LOGGING = H5E_LOGGING(); + /** Major error codes - Map */ + public static final long H5E_MAP = H5E_MAP(); + /** Minor error codes - File accessibility errors - File mount error */ public static final long H5E_MOUNT = H5E_MOUNT(); + /** Minor error codes - Parallel MPI - Some MPI function failed */ public static final long H5E_MPI = H5E_MPI(); + /** Minor error codes - Parallel MPI - MPI Error String */ public static final long H5E_MPIERRSTR = H5E_MPIERRSTR(); + /** Minor error codes - Link related errors - Too many soft links in path */ + public static final long H5E_NLINKS = H5E_NLINKS(); + /** Minor error codes - Parallel MPI - Can't perform independent IO */ + public static final long H5E_NO_INDEPENDENT = H5E_NO_INDEPENDENT(); + /** I/O pipeline errors - Filter present but encoding disabled */ + public static final long H5E_NOENCODER = H5E_NOENCODER(); + /** I/O pipeline errors - Requested filter is not available */ public static final long H5E_NOFILTER = H5E_NOFILTER(); + /** Minor error codes - Object atom related errors - Out of IDs for group */ public static final long H5E_NOIDS = H5E_NOIDS(); + /** Major error codes - No error */ public static final long H5E_NONE_MAJOR = H5E_NONE_MAJOR(); + /** No error */ public static final long H5E_NONE_MINOR = H5E_NONE_MINOR(); + /** Minor error codes - Resource errors - No space available for allocation */ public static final long H5E_NOSPACE = H5E_NOSPACE(); + /** Minor error codes - Cache related errors - Metadata not currently cached */ public static final long H5E_NOTCACHED = H5E_NOTCACHED(); + /** Minor error codes - B-tree related errors - Object not found */ public static final long H5E_NOTFOUND = H5E_NOTFOUND(); + /** Minor error codes - File accessibility errors - Not an HDF5 file */ public static final long H5E_NOTHDF5 = H5E_NOTHDF5(); + /** Minor error codes - Link related errors - Link class not registered */ + public static final long H5E_NOTREGISTERED = H5E_NOTREGISTERED(); + /** Minor error codes - Resource errors - Object is already open */ + public static final long H5E_OBJOPEN = H5E_OBJOPEN(); + /** Major error codes - Object header */ public static final long H5E_OHDR = H5E_OHDR(); + /** Minor error codes - Plugin errors - Can't open directory or file */ + public static final long H5E_OPENERROR = H5E_OPENERROR(); + /** Generic low-level file I/O errors - Address overflowed */ public static final long H5E_OVERFLOW = H5E_OVERFLOW(); + /** Major error codes - Page Buffering */ + public static final long H5E_PAGEBUF = H5E_PAGEBUF(); + /** Minor error codes - Group related errors - Problem with path to object */ + public static final long H5E_PATH = H5E_PATH(); + /** Major error codes - Data filters */ public static final long H5E_PLINE = H5E_PLINE(); + /** Major error codes - Property lists */ public static final long H5E_PLIST = H5E_PLIST(); + /** Major error codes - Plugin for dynamically loaded library */ + public static final long H5E_PLUGIN = H5E_PLUGIN(); + /** Minor error codes - Cache related errors - Protected metadata error */ public static final long H5E_PROTECT = H5E_PROTECT(); + /** Generic low-level file I/O errors - Read failed */ public static final long H5E_READERROR = H5E_READERROR(); + /** Major error codes - References */ public static final long H5E_REFERENCE = H5E_REFERENCE(); + /** Major error codes - Resource unavailable */ public static final long H5E_RESOURCE = H5E_RESOURCE(); + /** Major error codes - Reference Counted Strings */ public static final long H5E_RS = H5E_RS(); + /** Generic low-level file I/O errors - Seek failed */ public static final long H5E_SEEKERROR = H5E_SEEKERROR(); + /** Minor error codes - Property list errors - Disallowed operation */ + public static final long H5E_SETDISALLOWED = H5E_SETDISALLOWED(); + /** I/O pipeline errors - Error from filter 'set local' callback */ public static final long H5E_SETLOCAL = H5E_SETLOCAL(); + /** Major error codes - Skip Lists */ + public static final long H5E_SLIST = H5E_SLIST(); + /** Major error codes - Shared Object Header Messages */ + public static final long H5E_SOHM = H5E_SOHM(); + /** Major error codes - Data storage */ public static final long H5E_STORAGE = H5E_STORAGE(); + /** Major error codes - Symbol table */ public static final long H5E_SYM = H5E_SYM(); + /** Minor error codes - System level errors - System error message */ + public static final long H5E_SYSERRSTR = H5E_SYSERRSTR(); + /** Minor error codes - Cache related errors - Internal error detected */ + public static final long H5E_SYSTEM = H5E_SYSTEM(); + /** Minor error codes - Link related errors - Link traversal failure */ + public static final long H5E_TRAVERSE = H5E_TRAVERSE(); + /** Minor error codes - File accessibility errors - File has been truncated */ public static final long H5E_TRUNCATED = H5E_TRUNCATED(); + /** Major error codes - Ternary Search Trees */ public static final long H5E_TST = H5E_TST(); + /** Minor error codes - Argument errors - Information is uinitialized */ public static final long H5E_UNINITIALIZED = H5E_UNINITIALIZED(); + /** Minor error codes - Argument errors - Feature is unsupported */ public static final long H5E_UNSUPPORTED = H5E_UNSUPPORTED(); + /** Minor error codes - Object header related errors - Wrong version number */ public static final long H5E_VERSION = H5E_VERSION(); + /** Major error codes - Virtual File Layer */ public static final long H5E_VFL = H5E_VFL(); + /** Major error codes - Virtual Object Layer */ public static final long H5E_VOL = H5E_VOL(); + /** Error stack traversal direction - begin at API function, end deep */ public static final long H5E_WALK_DOWNWARD = H5E_WALK_DOWNWARD(); + /** Error stack traversal direction - begin deep, end at API function */ public static final long H5E_WALK_UPWARD = H5E_WALK_UPWARD(); + /** Generic low-level file I/O errors - Write failed */ public static final long H5E_WRITEERROR = H5E_WRITEERROR(); private static final int H5ES_STATUS_IN_PROGRESS = H5ES_STATUS_IN_PROGRESS(); @@ -423,29 +686,53 @@ public class HDF5Constants { public static final int H5R_OBJECT1 = H5R_OBJECT1(); public static final int H5R_OBJECT2 = H5R_OBJECT2(); + /** Define atomic datatypes */ public static final int H5S_ALL = H5S_ALL(); + /** Define user-level maximum number of dimensions */ public static final int H5S_MAX_RANK = H5S_MAX_RANK(); + /** Different types of dataspaces - error */ public static final int H5S_NO_CLASS = H5S_NO_CLASS(); + /** Different types of dataspaces - null dataspace */ public static final int H5S_NULL = H5S_NULL(); + /** Different types of dataspaces - scalar variable */ public static final int H5S_SCALAR = H5S_SCALAR(); + /** Enumerated type for the type of selection - Entire extent selected */ public static final int H5S_SEL_ALL = H5S_SEL_ALL(); + /** Enumerated type for the type of selection - Error */ public static final int H5S_SEL_ERROR = H5S_SEL_ERROR(); + /** Enumerated type for the type of selection - Hyperslab selected */ public static final int H5S_SEL_HYPERSLABS = H5S_SEL_HYPERSLABS(); + /** Enumerated type for the type of selection - LAST */ public static final int H5S_SEL_N = H5S_SEL_N(); + /** Enumerated type for the type of selection - Nothing selected */ public static final int H5S_SEL_NONE = H5S_SEL_NONE(); + /** Enumerated type for the type of selection - Points / elements selected */ public static final int H5S_SEL_POINTS = H5S_SEL_POINTS(); + /** Different ways of combining selections - Binary "and" operation for hyperslabs */ public static final int H5S_SELECT_AND = H5S_SELECT_AND(); + /** Different ways of combining selections - Append elements to end of point selection */ public static final int H5S_SELECT_APPEND = H5S_SELECT_APPEND(); + /** Different ways of combining selections - Invalid upper bound on selection operations */ public static final int H5S_SELECT_INVALID = H5S_SELECT_INVALID(); + /** Different ways of combining selections - error */ public static final int H5S_SELECT_NOOP = H5S_SELECT_NOOP(); + /** Different ways of combining selections - Binary "not" operation for hyperslabs */ public static final int H5S_SELECT_NOTA = H5S_SELECT_NOTA(); + /** Different ways of combining selections - Binary "not" operation for hyperslabs */ public static final int H5S_SELECT_NOTB = H5S_SELECT_NOTB(); + /** Different ways of combining selections - Binary "or" operation for hyperslabs */ public static final int H5S_SELECT_OR = H5S_SELECT_OR(); + /** Different ways of combining selections - Prepend elements to beginning of point selection */ public static final int H5S_SELECT_PREPEND = H5S_SELECT_PREPEND(); + /** Different ways of combining selections - Select "set" operation */ public static final int H5S_SELECT_SET = H5S_SELECT_SET(); + /** Different ways of combining selections - Binary "xor" operation for hyperslabs */ public static final int H5S_SELECT_XOR = H5S_SELECT_XOR(); + /** Different types of dataspaces - simple dataspace */ public static final int H5S_SIMPLE = H5S_SIMPLE(); + /** Define atomic datatypes */ public static final int H5S_UNLIMITED = H5S_UNLIMITED(); + public static final long H5T_ALPHA_B16 = H5T_ALPHA_B16(); public static final long H5T_ALPHA_B32 = H5T_ALPHA_B32(); public static final long H5T_ALPHA_B64 = H5T_ALPHA_B64(); @@ -664,48 +951,96 @@ public class HDF5Constants { public static final int H5_VOL_RESERVED = H5_VOL_RESERVED(); public static final int H5_VOL_MAX = H5_VOL_MAX(); + /** Return values for filter callback function */ public static final int H5Z_CB_CONT = H5Z_CB_CONT(); + /** Return values for filter callback function */ public static final int H5Z_CB_ERROR = H5Z_CB_ERROR(); + /** Return values for filter callback function */ public static final int H5Z_CB_FAIL = H5Z_CB_FAIL(); + /** Return values for filter callback function */ public static final int H5Z_CB_NO = H5Z_CB_NO(); + /** Values to decide if EDC is enabled for reading data */ public static final int H5Z_DISABLE_EDC = H5Z_DISABLE_EDC(); + /** Values to decide if EDC is enabled for reading data */ public static final int H5Z_ENABLE_EDC = H5Z_ENABLE_EDC(); + /** Values to decide if EDC is enabled for reading data */ public static final int H5Z_ERROR_EDC = H5Z_ERROR_EDC(); + /** Filter IDs - deflation like gzip */ public static final int H5Z_FILTER_DEFLATE = H5Z_FILTER_DEFLATE(); + /** Filter IDs - no filter */ public static final int H5Z_FILTER_ERROR = H5Z_FILTER_ERROR(); + /** Filter IDs - fletcher32 checksum of EDC */ public static final int H5Z_FILTER_FLETCHER32 = H5Z_FILTER_FLETCHER32(); + /** Filter IDs - maximum filter id */ public static final int H5Z_FILTER_MAX = H5Z_FILTER_MAX(); + /** Filter IDs - nbit compression */ public static final int H5Z_FILTER_NBIT = H5Z_FILTER_NBIT(); + /** Filter IDs - reserved indefinitely */ public static final int H5Z_FILTER_NONE = H5Z_FILTER_NONE(); + /** Filter IDs - filter ids below this value are reserved for library use */ public static final int H5Z_FILTER_RESERVED = H5Z_FILTER_RESERVED(); + /** Filter IDs - scale+offset compression */ public static final int H5Z_FILTER_SCALEOFFSET = H5Z_FILTER_SCALEOFFSET(); + /** Filter IDs - shuffle the data */ public static final int H5Z_FILTER_SHUFFLE = H5Z_FILTER_SHUFFLE(); + /** Filter IDs - szip compression */ public static final int H5Z_FILTER_SZIP = H5Z_FILTER_SZIP(); + /** Flags for filter definition (stored) + * definition flag mask */ public static final int H5Z_FLAG_DEFMASK = H5Z_FLAG_DEFMASK(); + /** Additional flags for filter invocation (not stored) + * invocation flag mask */ public static final int H5Z_FLAG_INVMASK = H5Z_FLAG_INVMASK(); + /** Flags for filter definition (stored) + * filter is mandatory */ public static final int H5Z_FLAG_MANDATORY = H5Z_FLAG_MANDATORY(); + /** Flags for filter definition (stored) + * filter is optional */ public static final int H5Z_FLAG_OPTIONAL = H5Z_FLAG_OPTIONAL(); + /** Additional flags for filter invocation (not stored) + * reverse direction; read */ public static final int H5Z_FLAG_REVERSE = H5Z_FLAG_REVERSE(); + /** Additional flags for filter invocation (not stored) + * skip EDC filters for read */ public static final int H5Z_FLAG_SKIP_EDC = H5Z_FLAG_SKIP_EDC(); + /** Symbol to remove all filters in H5Premove_filter */ + public static final int H5Z_FILTER_ALL = H5Z_FILTER_ALL(); + /** Maximum number of filters allowed in a pipeline */ public static final int H5Z_MAX_NFILTERS = H5Z_MAX_NFILTERS(); + /** Values to decide if EDC is enabled for reading data */ public static final int H5Z_NO_EDC = H5Z_NO_EDC(); + /** Bit flags for H5Zget_filter_info */ public static final int H5Z_FILTER_CONFIG_ENCODE_ENABLED = H5Z_FILTER_CONFIG_ENCODE_ENABLED(); + /** Bit flags for H5Zget_filter_info */ public static final int H5Z_FILTER_CONFIG_DECODE_ENABLED = H5Z_FILTER_CONFIG_DECODE_ENABLED(); + /** Special parameters for ScaleOffset filter*/ public static final int H5Z_SO_INT_MINBITS_DEFAULT = H5Z_SO_INT_MINBITS_DEFAULT(); + /** Special parameters for ScaleOffset filter*/ public static final int H5Z_SO_FLOAT_DSCALE = H5Z_SO_FLOAT_DSCALE(); + /** Special parameters for ScaleOffset filter*/ public static final int H5Z_SO_FLOAT_ESCALE = H5Z_SO_FLOAT_ESCALE(); + /** Special parameters for ScaleOffset filter*/ public static final int H5Z_SO_INT = H5Z_SO_INT(); + /** shuffle filter - Number of parameters that users can set */ public static final int H5Z_SHUFFLE_USER_NPARMS = H5Z_SHUFFLE_USER_NPARMS(); + /** shuffle filter - Total number of parameters for filter */ public static final int H5Z_SHUFFLE_TOTAL_NPARMS = H5Z_SHUFFLE_TOTAL_NPARMS(); + /** szip filter - Number of parameters that users can set */ public static final int H5Z_SZIP_USER_NPARMS = H5Z_SZIP_USER_NPARMS(); + /** szip filter - Total number of parameters for filter */ public static final int H5Z_SZIP_TOTAL_NPARMS = H5Z_SZIP_TOTAL_NPARMS(); + /** szip filter - "User" parameter for option mask */ public static final int H5Z_SZIP_PARM_MASK = H5Z_SZIP_PARM_MASK(); + /** szip filter - "User" parameter for pixels-per-block */ public static final int H5Z_SZIP_PARM_PPB = H5Z_SZIP_PARM_PPB(); + /** szip filter - "Local" parameter for bits-per-pixel */ public static final int H5Z_SZIP_PARM_BPP = H5Z_SZIP_PARM_BPP(); + /** szip filter - "Local" parameter for pixels-per-scanline */ public static final int H5Z_SZIP_PARM_PPS = H5Z_SZIP_PARM_PPS(); + /** nbit filter - Number of parameters that users can set */ public static final int H5Z_NBIT_USER_NPARMS = H5Z_NBIT_USER_NPARMS(); + /** scale offset filter - Number of parameters that users can set */ public static final int H5Z_SCALEOFFSET_USER_NPARMS = H5Z_SCALEOFFSET_USER_NPARMS(); - public static final int H5Z_FILTER_ALL = H5Z_FILTER_ALL(); // ///////////////////////////////////////////////////////////////////////// // List of private native variables to get constant values from C // @@ -840,6 +1175,8 @@ public class HDF5Constants { private static native final long H5E_BADGROUP(); + private static native final long H5E_BADITER(); + private static native final long H5E_BADMESG(); private static native final long H5E_BADRANGE(); @@ -860,15 +1197,30 @@ public class HDF5Constants { private static native final long H5E_CANAPPLY(); - // private static native final long H5E_CANTALLOC(); + private static native final long H5E_CANTALLOC(); + + private static native final long H5E_CANTAPPEND(); + + private static native final long H5E_CANTATTACH(); + + private static native final long H5E_CANTCLEAN(); + private static native final long H5E_CANTCLIP(); private static native final long H5E_CANTCLOSEFILE(); + private static native final long H5E_CANTCLOSEOBJ(); + + private static native final long H5E_CANTCOMPARE(); + + private static native final long H5E_CANTCOMPUTE(); + private static native final long H5E_CANTCONVERT(); private static native final long H5E_CANTCOPY(); + private static native final long H5E_CANTCORK(); + private static native final long H5E_CANTCOUNT(); private static native final long H5E_CANTCREATE(); @@ -881,18 +1233,36 @@ public class HDF5Constants { private static native final long H5E_CANTDELETEFILE(); + private static native final long H5E_CANTDEPEND(); + + private static native final long H5E_CANTDIRTY(); + private static native final long H5E_CANTENCODE(); + private static native final long H5E_CANTEXPUNGE(); + + private static native final long H5E_CANTEXTEND(); + + private static native final long H5E_CANTFILTER(); + private static native final long H5E_CANTFLUSH(); private static native final long H5E_CANTFREE(); + private static native final long H5E_CANTGATHER(); + + private static native final long H5E_CANTGC(); + private static native final long H5E_CANTGET(); + private static native final long H5E_CANTGETSIZE(); + private static native final long H5E_CANTINC(); private static native final long H5E_CANTINIT(); + private static native final long H5E_CANTINS(); + private static native final long H5E_CANTINSERT(); private static native final long H5E_CANTLIST(); @@ -901,29 +1271,96 @@ public class HDF5Constants { private static native final long H5E_CANTLOCK(); + private static native final long H5E_CANTLOCKFILE(); + + private static native final long H5E_CANTMARKCLEAN(); + + private static native final long H5E_CANTMARKDIRTY(); + + private static native final long H5E_CANTMARKSERIALIZED(); + + private static native final long H5E_CANTMARKUNSERIALIZED(); + + private static native final long H5E_CANTMERGE(); + + private static native final long H5E_CANTMOVE(); + + private static native final long H5E_CANTMODIFY(); + private static native final long H5E_CANTNEXT(); + private static native final long H5E_CANTNOTIFY(); + private static native final long H5E_CANTOPENFILE(); private static native final long H5E_CANTOPENOBJ(); - // private static native final long H5E_CANTRECV(); + private static native final long H5E_CANTOPERATE(); + + private static native final long H5E_CANTPACK(); + + private static native final long H5E_CANTPIN(); + + private static native final long H5E_CANTPROTECT(); + + private static native final long H5E_CANTRECV(); + + private static native final long H5E_CANTREDISTRIBUTE(); + private static native final long H5E_CANTREGISTER(); private static native final long H5E_CANTRELEASE(); + private static native final long H5E_CANTREMOVE(); + + private static native final long H5E_CANTRENAME(); + + private static native final long H5E_CANTRESET(); + + private static native final long H5E_CANTRESIZE(); + + private static native final long H5E_CANTRESTORE(); + + private static native final long H5E_CANTREVIVE(); + + private static native final long H5E_CANTSHRINK(); + private static native final long H5E_CANTSELECT(); private static native final long H5E_CANTSET(); + private static native final long H5E_CANTSERIALIZE(); + + private static native final long H5E_CANTSORT(); + private static native final long H5E_CANTSPLIT(); + private static native final long H5E_CANTSWAP(); + + private static native final long H5E_CANTTAG(); + + private static native final long H5E_CANTUNCORK(); + + private static native final long H5E_CANTUNDEPEND(); + private static native final long H5E_CANTUNLOCK(); + private static native final long H5E_CANTUNLOCKFILE(); + + private static native final long H5E_CANTUNPIN(); + + private static native final long H5E_CANTUNPROTECT(); + + private static native final long H5E_CANTUNSERIALIZE(); + + private static native final long H5E_CANTUPDATE(); + private static native final long H5E_CLOSEERROR(); private static native final long H5E_COMPLEN(); + private static native final long H5E_CONTEXT(); + private static native final long H5E_DATASET(); private static native final long H5E_DATASPACE(); @@ -934,10 +1371,16 @@ public class HDF5Constants { private static native final long H5E_DUPCLASS(); + private static native final long H5E_EARRAY(); + private static native final long H5E_EFL(); + private static native final long H5E_ERROR(); + private static native final long H5E_EXISTS(); + private static native final long H5E_FARRAY(); + private static native final long H5E_FCNTL(); private static native final long H5E_FILE(); @@ -946,10 +1389,14 @@ public class HDF5Constants { private static native final long H5E_FILEOPEN(); + private static native final long H5E_FSPACE(); + private static native final long H5E_FUNC(); private static native final long H5E_HEAP(); + private static native final long H5E_INCONSISTENTSTATE(); + private static native final long H5E_INTERNAL(); private static native final long H5E_IO(); @@ -958,8 +1405,12 @@ public class HDF5Constants { private static native final long H5E_LINKCOUNT(); + private static native final long H5E_LOGGING(); + private static native final int H5E_MAJOR(); + private static native final long H5E_MAP(); + private static native final int H5E_MINOR(); private static native final long H5E_MOUNT(); @@ -968,6 +1419,12 @@ public class HDF5Constants { private static native final long H5E_MPIERRSTR(); + private static native final long H5E_NLINKS(); + + private static native final long H5E_NO_INDEPENDENT(); + + private static native final long H5E_NOENCODER(); + private static native final long H5E_NOFILTER(); private static native final long H5E_NOIDS(); @@ -984,14 +1441,26 @@ public class HDF5Constants { private static native final long H5E_NOTHDF5(); + private static native final long H5E_NOTREGISTERED(); + + private static native final long H5E_OBJOPEN(); + private static native final long H5E_OHDR(); + private static native final long H5E_OPENERROR(); + private static native final long H5E_OVERFLOW(); + private static native final long H5E_PAGEBUF(); + + private static native final long H5E_PATH(); + private static native final long H5E_PLINE(); private static native final long H5E_PLIST(); + private static native final long H5E_PLUGIN(); + private static native final long H5E_PROTECT(); private static native final long H5E_READERROR(); @@ -1004,12 +1473,24 @@ public class HDF5Constants { private static native final long H5E_SEEKERROR(); + private static native final long H5E_SETDISALLOWED(); + private static native final long H5E_SETLOCAL(); + private static native final long H5E_SLIST(); + + private static native final long H5E_SOHM(); + private static native final long H5E_STORAGE(); private static native final long H5E_SYM(); + private static native final long H5E_SYSERRSTR(); + + private static native final long H5E_SYSTEM(); + + private static native final long H5E_TRAVERSE(); + private static native final long H5E_TRUNCATED(); private static native final long H5E_TST(); diff --git a/java/src/hdf/hdf5lib/HDF5GroupInfo.java b/java/src/hdf/hdf5lib/HDF5GroupInfo.java index a45cb7c..4c31af7 100644 --- a/java/src/hdf/hdf5lib/HDF5GroupInfo.java +++ b/java/src/hdf/hdf5lib/HDF5GroupInfo.java @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -41,6 +41,8 @@ public class HDF5GroupInfo { long mtime; int linklen; + /** Container for the information reported about an HDF5 Object + * from the H5Gget_obj_info() method */ public HDF5GroupInfo() { fileno = new long[2]; objno = new long[2]; @@ -88,27 +90,44 @@ public class HDF5GroupInfo { linklen = 0; } - /* accessors */ + /** fileno accessors + * @return the file number if successful + */ public long[] getFileno() { return fileno; } + /** accessors + * @return the object number if successful + */ public long[] getObjno() { return objno; } + /** accessors + * @return type of group if successful + */ public int getType() { return type; } + /** accessors + * @return the number of links in the group if successful + */ public int getNlink() { return nlink; } + /** accessors + * @return the modified time value if successful + */ public long getMtime() { return mtime; } + /** accessors + * @return a length of link name if successful + */ public int getLinklen() { return linklen; } diff --git a/java/src/hdf/hdf5lib/HDFArray.java b/java/src/hdf/hdf5lib/HDFArray.java index 30f0fc8..bb9357e 100644 --- a/java/src/hdf/hdf5lib/HDFArray.java +++ b/java/src/hdf/hdf5lib/HDFArray.java @@ -6,33 +6,30 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - package hdf.hdf5lib; import hdf.hdf5lib.exceptions.HDF5Exception; import hdf.hdf5lib.exceptions.HDF5JavaException; +import java.util.Arrays; /** * This is a class for handling multidimensional arrays for HDF. * <p> - * The purpose is to allow the storage and retrieval of arbitrary array types - * containing scientific data. + * The purpose is to allow the storage and retrieval of arbitrary array types containing scientific data. * <p> - * The methods support the conversion of an array to and from Java to a - * one-dimensional array of bytes suitable for I/O by the C library. + * The methods support the conversion of an array to and from Java to a one-dimensional array of bytes suitable for I/O + * by the C library. * <p> - * This class heavily uses the <a - * href="./hdf.hdf5lib.HDFNativeData.html">HDFNativeData</a> class to - * convert between Java and C representations. + * This class heavily uses the <a href="./hdf.hdf5lib.HDFNativeData.html">HDFNativeData</a> class to convert between + * Java and C representations. */ public class HDFArray { - private Object _theArray = null; private ArrayDescriptor _desc = null; private byte[] _barray = null; @@ -40,31 +37,27 @@ public class HDFArray { // public HDFArray() {} /** - * The input must be a Java Array (possibly multidimensional) of primitive - * numbers or sub-classes of Number. + * The input must be a Java Array (possibly multidimensional) of primitive numbers or sub-classes of Number. * <p> - * The input is analysed to determine the number of dimensions and size of - * each dimension, as well as the type of the elements. + * The input is analysed to determine the number of dimensions and size of each dimension, as well as the type of + * the elements. * <p> * The description is saved in private variables, and used to convert data. * * @param anArray - * The array object. - * + * The array object. * @exception hdf.hdf5lib.exceptions.HDF5Exception - * object is not an array. + * object is not an array. */ - public HDFArray(Object anArray) throws HDF5Exception { - + public HDFArray(Object anArray) throws HDF5Exception + { if (anArray == null) { - HDF5JavaException ex = new HDF5JavaException( - "HDFArray: array is null?: "); + HDF5JavaException ex = new HDF5JavaException("HDFArray: array is null?: "); } Class tc = anArray.getClass(); if (tc.isArray() == false) { /* exception: not an array */ - HDF5JavaException ex = new HDF5JavaException( - "HDFArray: not an array?: "); + HDF5JavaException ex = new HDF5JavaException("HDFArray: not an array?: "); throw (ex); } _theArray = anArray; @@ -72,8 +65,7 @@ public class HDFArray { /* extra error checking -- probably not needed */ if (_desc == null) { - HDF5JavaException ex = new HDF5JavaException( - "HDFArray: internal error: array description failed?: "); + HDF5JavaException ex = new HDF5JavaException("HDFArray: internal error: array description failed?: "); throw (ex); } } @@ -81,49 +73,48 @@ public class HDFArray { /** * Allocate a one-dimensional array of bytes sufficient to store the array. * - * @return A one-D array of bytes, filled with zeroes. The bytes are - * sufficient to hold the data of the Array passed to the - * constructor. + * @return A one-D array of bytes, filled with zeroes. The bytes are sufficient to hold the data of the Array passed + * to the constructor. * @exception hdf.hdf5lib.exceptions.HDF5JavaException - * Allocation failed. + * Allocation failed. */ - public byte[] emptyBytes() throws HDF5JavaException { + public byte[] emptyBytes() + throws HDF5JavaException + { byte[] b = null; - if ((ArrayDescriptor.dims == 1) && (ArrayDescriptor.NT == 'B')) { + if ((ArrayDescriptor.dims == 1) + && (ArrayDescriptor.NT == 'B')) { b = (byte[]) _theArray; } else { b = new byte[ArrayDescriptor.totalSize]; } if (b == null) { - HDF5JavaException ex = new HDF5JavaException( - "HDFArray: emptyBytes: allocation failed"); + HDF5JavaException ex = new HDF5JavaException("HDFArray: emptyBytes: allocation failed"); throw (ex); } return (b); } /** - * Given a Java array of numbers, convert it to a one-dimensional array of - * bytes in correct native order. + * Given a Java array of numbers, convert it to a one-dimensional array of bytes in correct native order. * - * @return A one-D array of bytes, constructed from the Array passed to the - * constructor. + * @return A one-D array of bytes, constructed from the Array passed to the constructor. * @exception hdf.hdf5lib.exceptions.HDF5JavaException - * the object not an array or other internal error. + * the object not an array or other internal error. */ - public byte[] byteify() throws HDF5JavaException { - + public byte[] byteify() + throws HDF5JavaException + { if (_barray != null) { return _barray; } if (_theArray == null) { /* exception: not an array */ - HDF5JavaException ex = new HDF5JavaException( - "HDFArray: byteify not an array?: "); + HDF5JavaException ex = new HDF5JavaException("HDFArray: byteify not an array?: "); throw (ex); } @@ -140,73 +131,53 @@ public class HDFArray { byte[] therow; if (ArrayDescriptor.NT == 'I') { - therow = HDFNativeData.intToByte(0, - ArrayDescriptor.dimlen[1], (int[]) _theArray); + therow = HDFNativeData.intToByte(0, ArrayDescriptor.dimlen[1], (int[]) _theArray); } else if (ArrayDescriptor.NT == 'S') { - therow = HDFNativeData.shortToByte(0, - ArrayDescriptor.dimlen[1], (short[]) _theArray); + therow = HDFNativeData.shortToByte(0, ArrayDescriptor.dimlen[1], (short[]) _theArray); } else if (ArrayDescriptor.NT == 'F') { - therow = HDFNativeData.floatToByte(0, - ArrayDescriptor.dimlen[1], (float[]) _theArray); + therow = HDFNativeData.floatToByte(0, ArrayDescriptor.dimlen[1], (float[]) _theArray); } else if (ArrayDescriptor.NT == 'J') { - therow = HDFNativeData.longToByte(0, - ArrayDescriptor.dimlen[1], (long[]) _theArray); + therow = HDFNativeData.longToByte(0, ArrayDescriptor.dimlen[1], (long[]) _theArray); } else if (ArrayDescriptor.NT == 'D') { - therow = HDFNativeData - .doubleToByte(0, ArrayDescriptor.dimlen[1], - (double[]) _theArray); + therow = HDFNativeData.doubleToByte(0, ArrayDescriptor.dimlen[1], (double[]) _theArray); } else if (ArrayDescriptor.NT == 'L') { if (ArrayDescriptor.className.equals("java.lang.Byte")) { therow = ByteObjToByte((Byte[]) _theArray); } - else if (ArrayDescriptor.className - .equals("java.lang.Integer")) { + else if (ArrayDescriptor.className.equals("java.lang.Integer")) { therow = IntegerToByte((Integer[]) _theArray); } - else if (ArrayDescriptor.className - .equals("java.lang.Short")) { + else if (ArrayDescriptor.className.equals("java.lang.Short")) { therow = ShortToByte((Short[]) _theArray); } - else if (ArrayDescriptor.className - .equals("java.lang.Float")) { + else if (ArrayDescriptor.className.equals("java.lang.Float")) { therow = FloatObjToByte((Float[]) _theArray); } - else if (ArrayDescriptor.className - .equals("java.lang.Double")) { + else if (ArrayDescriptor.className.equals("java.lang.Double")) { therow = DoubleObjToByte((Double[]) _theArray); } - else if (ArrayDescriptor.className - .equals("java.lang.Long")) { + else if (ArrayDescriptor.className.equals("java.lang.Long")) { therow = LongObjToByte((Long[]) _theArray); } else { - HDF5JavaException ex = new HDF5JavaException( - "HDFArray: unknown type of Object?"); + HDF5JavaException ex = new HDF5JavaException("HDFArray: unknown type of Object?"); throw (ex); } } else { - HDF5JavaException ex = new HDF5JavaException( - "HDFArray: unknown type of data?"); + HDF5JavaException ex = new HDF5JavaException("HDFArray: unknown type of data?"); throw (ex); } - System - .arraycopy( - therow, - 0, - _barray, - 0, - (ArrayDescriptor.dimlen[1] * ArrayDescriptor.NTsize)); + System.arraycopy(therow, 0, _barray, 0, (ArrayDescriptor.dimlen[1] * ArrayDescriptor.NTsize)); return _barray; } catch (OutOfMemoryError err) { - HDF5JavaException ex = new HDF5JavaException( - "HDFArray: byteify array too big?"); + HDF5JavaException ex = new HDF5JavaException("HDFArray: byteify array too big?"); throw (ex); } } @@ -216,8 +187,7 @@ public class HDFArray { _barray = new byte[ArrayDescriptor.totalSize]; } catch (OutOfMemoryError err) { - HDF5JavaException ex = new HDF5JavaException( - "HDFArray: byteify array too big?"); + HDF5JavaException ex = new HDF5JavaException("HDFArray: byteify array too big?"); throw (ex); } @@ -240,8 +210,7 @@ public class HDFArray { else { /* check range of index */ if (index > (ArrayDescriptor.dimlen[i] - 1)) { - throw new java.lang.IndexOutOfBoundsException( - "HDFArray: byteify index OOB?"); + throw new java.lang.IndexOutOfBoundsException("HDFArray: byteify index OOB?"); } oo = java.lang.reflect.Array.get(oo, index); ArrayDescriptor.currentindex[i] = index; @@ -253,242 +222,187 @@ public class HDFArray { byte arow[]; try { if (ArrayDescriptor.NT == 'J') { - arow = HDFNativeData - .longToByte( - 0, - ArrayDescriptor.dimlen[ArrayDescriptor.dims], - (long[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); - arow = HDFNativeData - .longToByte( - 0, - ArrayDescriptor.dimlen[ArrayDescriptor.dims], - (long[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); + arow = HDFNativeData.longToByte(0, ArrayDescriptor.dimlen[ArrayDescriptor.dims], + (long[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); + arow = HDFNativeData.longToByte(0, ArrayDescriptor.dimlen[ArrayDescriptor.dims], + (long[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else if (ArrayDescriptor.NT == 'I') { - arow = HDFNativeData - .intToByte( - 0, - ArrayDescriptor.dimlen[ArrayDescriptor.dims], - (int[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); + arow = HDFNativeData.intToByte(0, ArrayDescriptor.dimlen[ArrayDescriptor.dims], + (int[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else if (ArrayDescriptor.NT == 'S') { - arow = HDFNativeData - .shortToByte( - 0, - ArrayDescriptor.dimlen[ArrayDescriptor.dims], - (short[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); + arow = HDFNativeData.shortToByte(0, ArrayDescriptor.dimlen[ArrayDescriptor.dims], + (short[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else if (ArrayDescriptor.NT == 'B') { arow = (byte[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]; } else if (ArrayDescriptor.NT == 'F') { /* 32 bit float */ - arow = HDFNativeData - .floatToByte( - 0, - ArrayDescriptor.dimlen[ArrayDescriptor.dims], - (float[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); + arow = HDFNativeData.floatToByte(0, ArrayDescriptor.dimlen[ArrayDescriptor.dims], + (float[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else if (ArrayDescriptor.NT == 'D') { /* 64 bit float */ - arow = HDFNativeData - .doubleToByte( - 0, - ArrayDescriptor.dimlen[ArrayDescriptor.dims], - (double[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); + arow = HDFNativeData.doubleToByte(0, ArrayDescriptor.dimlen[ArrayDescriptor.dims], + (double[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else if (ArrayDescriptor.NT == 'L') { if (ArrayDescriptor.className.equals("java.lang.Byte")) { arow = ByteObjToByte((Byte[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } - else if (ArrayDescriptor.className - .equals("java.lang.Integer")) { + else if (ArrayDescriptor.className.equals("java.lang.Integer")) { arow = IntegerToByte((Integer[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } - else if (ArrayDescriptor.className - .equals("java.lang.Short")) { + else if (ArrayDescriptor.className.equals("java.lang.Short")) { arow = ShortToByte((Short[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } - else if (ArrayDescriptor.className - .equals("java.lang.Float")) { + else if (ArrayDescriptor.className.equals("java.lang.Float")) { arow = FloatObjToByte((Float[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } - else if (ArrayDescriptor.className - .equals("java.lang.Double")) { + else if (ArrayDescriptor.className.equals("java.lang.Double")) { arow = DoubleObjToByte((Double[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else if (ArrayDescriptor.className.equals("java.lang.Long")) { arow = LongObjToByte((Long[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else { - HDF5JavaException ex = new HDF5JavaException( - "HDFArray: byteify Object type not implemented?"); + HDF5JavaException ex = new HDF5JavaException("HDFArray: byteify Object type not implemented?"); throw (ex); } } else { - HDF5JavaException ex = new HDF5JavaException( - "HDFArray: byteify unknown type not implemented?"); + HDF5JavaException ex = new HDF5JavaException("HDFArray: byteify unknown type not implemented?"); throw (ex); } - System - .arraycopy( - arow, - 0, - _barray, - n, - (ArrayDescriptor.dimlen[ArrayDescriptor.dims] * ArrayDescriptor.NTsize)); + System.arraycopy(arow, 0, _barray, n, + (ArrayDescriptor.dimlen[ArrayDescriptor.dims] * ArrayDescriptor.NTsize)); n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1]; } catch (OutOfMemoryError err) { - HDF5JavaException ex = new HDF5JavaException( - "HDFArray: byteify array too big?"); + HDF5JavaException ex = new HDF5JavaException("HDFArray: byteify array too big?"); throw (ex); } } /* assert: the whole array is completed--currentindex should == len - 1 */ - /* error checks */ - if (n < ArrayDescriptor.totalSize) { - throw new java.lang.InternalError(new String( - "HDFArray::byteify: Panic didn't complete all input data: n= " - + n + " size = " + ArrayDescriptor.totalSize)); + throw new java.lang.InternalError(new String("HDFArray::byteify: Panic didn't complete all input data: n= " + + n + " size = " + ArrayDescriptor.totalSize)); } for (i = 0; i < ArrayDescriptor.dims; i++) { if (ArrayDescriptor.currentindex[i] != ArrayDescriptor.dimlen[i] - 1) { throw new java.lang.InternalError(new String( - "Panic didn't complete all data: currentindex[" + i - + "] = " + ArrayDescriptor.currentindex[i] - + " (should be " - + (ArrayDescriptor.dimlen[i] - 1) + " ?)")); + "Panic didn't complete all data: currentindex[" + i + "] = " + ArrayDescriptor.currentindex[i] + + " (should be " + (ArrayDescriptor.dimlen[i] - 1) + " ?)")); } } return _barray; } /** - * Given a one-dimensional array of bytes representing numbers, convert it - * to a java array of the shape and size passed to the constructor. + * Given a one-dimensional array of bytes representing numbers, convert it to a java array of the shape and size + * passed to the constructor. * * @param bytes - * The bytes to construct the Array. - * @return An Array (possibly multidimensional) of primitive or number - * objects. - * @exception hdf.hdf5lib.exceptions.HDF5JavaException - * the object not an array or other internal error. + * The bytes to construct the Array. + * @return + * An Array (possibly multidimensional) of primitive or number objects. + * @exception + * hdf.hdf5lib.exceptions.HDF5JavaException the object not an array or other internal error. */ - public Object arrayify(byte[] bytes) throws HDF5JavaException { - + public Object arrayify(byte[] bytes) throws HDF5JavaException + { if (_theArray == null) { /* exception: not an array */ - HDF5JavaException ex = new HDF5JavaException( - "arrayify: not an array?: "); + HDF5JavaException ex = new HDF5JavaException("arrayify: not an array?: "); throw (ex); } if (java.lang.reflect.Array.getLength(bytes) != ArrayDescriptor.totalSize) { /* exception: array not right size */ - HDF5JavaException ex = new HDF5JavaException( - "arrayify: array is wrong size?: "); + HDF5JavaException ex = new HDF5JavaException("arrayify: array is wrong size?: "); throw (ex); } _barray = bytes; /* hope that the bytes are correct.... */ + if (ArrayDescriptor.dims == 1) { /* special case */ /* 2 data copies here! */ try { if (ArrayDescriptor.NT == 'I') { int[] x = HDFNativeData.byteToInt(_barray); - System.arraycopy(x, 0, _theArray, 0, - ArrayDescriptor.dimlen[1]); + System.arraycopy(x, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } else if (ArrayDescriptor.NT == 'S') { short[] x = HDFNativeData.byteToShort(_barray); - System.arraycopy(x, 0, _theArray, 0, - ArrayDescriptor.dimlen[1]); + System.arraycopy(x, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } else if (ArrayDescriptor.NT == 'F') { float x[] = HDFNativeData.byteToFloat(_barray); - System.arraycopy(x, 0, _theArray, 0, - ArrayDescriptor.dimlen[1]); + System.arraycopy(x, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } else if (ArrayDescriptor.NT == 'J') { long x[] = HDFNativeData.byteToLong(_barray); - System.arraycopy(x, 0, _theArray, 0, - ArrayDescriptor.dimlen[1]); + System.arraycopy(x, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } else if (ArrayDescriptor.NT == 'D') { double x[] = HDFNativeData.byteToDouble(_barray); - System.arraycopy(x, 0, _theArray, 0, - ArrayDescriptor.dimlen[1]); + System.arraycopy(x, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } else if (ArrayDescriptor.NT == 'B') { - System.arraycopy(_barray, 0, _theArray, 0, - ArrayDescriptor.dimlen[1]); + System.arraycopy(_barray, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } else if (ArrayDescriptor.NT == 'L') { if (ArrayDescriptor.className.equals("java.lang.Byte")) { Byte I[] = ByteToByteObj(_barray); - System.arraycopy(I, 0, _theArray, 0, - ArrayDescriptor.dimlen[1]); + System.arraycopy(I, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } - else if (ArrayDescriptor.className - .equals("java.lang.Integer")) { + else if (ArrayDescriptor.className.equals("java.lang.Integer")) { Integer I[] = ByteToInteger(_barray); - System.arraycopy(I, 0, _theArray, 0, - ArrayDescriptor.dimlen[1]); + System.arraycopy(I, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } - else if (ArrayDescriptor.className - .equals("java.lang.Short")) { + else if (ArrayDescriptor.className.equals("java.lang.Short")) { Short I[] = ByteToShort(_barray); - System.arraycopy(I, 0, _theArray, 0, - ArrayDescriptor.dimlen[1]); + System.arraycopy(I, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } - else if (ArrayDescriptor.className - .equals("java.lang.Float")) { + else if (ArrayDescriptor.className.equals("java.lang.Float")) { Float I[] = ByteToFloatObj(_barray); - System.arraycopy(I, 0, _theArray, 0, - ArrayDescriptor.dimlen[1]); + System.arraycopy(I, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } - else if (ArrayDescriptor.className - .equals("java.lang.Double")) { + else if (ArrayDescriptor.className.equals("java.lang.Double")) { Double I[] = ByteToDoubleObj(_barray); - System.arraycopy(I, 0, _theArray, 0, - ArrayDescriptor.dimlen[1]); + System.arraycopy(I, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } else if (ArrayDescriptor.className.equals("java.lang.Long")) { Long I[] = ByteToLongObj(_barray); - System.arraycopy(I, 0, _theArray, 0, - ArrayDescriptor.dimlen[1]); + System.arraycopy(I, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } else { - HDF5JavaException ex = new HDF5JavaException( - "arrayify: Object type not implemented yet..."); + HDF5JavaException ex = new HDF5JavaException("arrayify: Object type not implemented yet..."); throw (ex); } } else { - HDF5JavaException ex = new HDF5JavaException( - "arrayify: unknown type not implemented yet..."); + HDF5JavaException ex = new HDF5JavaException("arrayify: unknown type not implemented yet..."); throw (ex); } } catch (OutOfMemoryError err) { - HDF5JavaException ex = new HDF5JavaException( - "HDFArray: arrayify array too big?"); + HDF5JavaException ex = new HDF5JavaException("HDFArray: arrayify array too big?"); throw (ex); } } @@ -496,8 +410,54 @@ public class HDFArray { Object oo = _theArray; int n = 0; /* the current byte */ + int m = 0; /* the current array index */ int index = 0; int i; + Object flattenedArray = null; + + switch (ArrayDescriptor.NT) { + case 'J': + flattenedArray = (Object) HDFNativeData.byteToLong(_barray); + break; + case 'S': + flattenedArray = (Object) HDFNativeData.byteToShort(_barray); + break; + case 'I': + flattenedArray = (Object) HDFNativeData.byteToInt(_barray); + break; + case 'F': + flattenedArray = (Object) HDFNativeData.byteToFloat(_barray); + break; + case 'D': + flattenedArray = (Object) HDFNativeData.byteToDouble(_barray); + break; + case 'B': + flattenedArray = (Object) _barray; + break; + case 'L': + { + if (ArrayDescriptor.className.equals("java.lang.Byte")) + flattenedArray = (Object) ByteToByteObj(_barray); + else if (ArrayDescriptor.className.equals("java.lang.Short")) + flattenedArray = (Object) ByteToShort(_barray); + else if (ArrayDescriptor.className.equals("java.lang.Integer")) + flattenedArray = (Object) ByteToInteger(_barray); + else if (ArrayDescriptor.className.equals("java.lang.Long")) + flattenedArray = (Object) ByteToLongObj(_barray); + else if (ArrayDescriptor.className.equals("java.lang.Float")) + flattenedArray = (Object) ByteToFloatObj(_barray); + else if (ArrayDescriptor.className.equals("java.lang.Double")) + flattenedArray = (Object) ByteToDoubleObj(_barray); + else { + HDF5JavaException ex = new HDF5JavaException("HDFArray: unsupported Object type: " + ArrayDescriptor.NT); + throw (ex); + } + } // end of statement for arrays of boxed objects + default: + HDF5JavaException ex = new HDF5JavaException("HDFArray: unknown or unsupported type: " + ArrayDescriptor.NT); + throw (ex); + } // end of switch statement for arrays of primitives + while (n < ArrayDescriptor.totalSize) { oo = ArrayDescriptor.objs[0]; index = n / ArrayDescriptor.bytetoindex[0]; @@ -524,222 +484,86 @@ public class HDFArray { /* array-ify */ try { - if (ArrayDescriptor.NT == 'J') { - long[] arow = HDFNativeData.byteToLong(n, - ArrayDescriptor.dimlen[ArrayDescriptor.dims], - _barray); - java.lang.reflect.Array - .set( - ArrayDescriptor.objs[ArrayDescriptor.dims - 2], - (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]), - arow); - n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1]; - ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++; - } - else if (ArrayDescriptor.NT == 'I') { - int[] arow = HDFNativeData.byteToInt(n, - ArrayDescriptor.dimlen[ArrayDescriptor.dims], - _barray); - java.lang.reflect.Array - .set( - ArrayDescriptor.objs[ArrayDescriptor.dims - 2], - (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]), - arow); - - n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1]; - ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++; - } - else if (ArrayDescriptor.NT == 'S') { - short[] arow = HDFNativeData.byteToShort(n, - ArrayDescriptor.dimlen[ArrayDescriptor.dims], - _barray); - java.lang.reflect.Array - .set( - ArrayDescriptor.objs[ArrayDescriptor.dims - 2], - (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]), - arow); - - n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1]; - ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++; - } - else if (ArrayDescriptor.NT == 'B') { - System.arraycopy(_barray, n, - ArrayDescriptor.objs[ArrayDescriptor.dims - 1], 0, - ArrayDescriptor.dimlen[ArrayDescriptor.dims]); - n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1]; - } - else if (ArrayDescriptor.NT == 'F') { - float arow[] = HDFNativeData.byteToFloat(n, - ArrayDescriptor.dimlen[ArrayDescriptor.dims], - _barray); - java.lang.reflect.Array - .set( - ArrayDescriptor.objs[ArrayDescriptor.dims - 2], - (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]), - arow); - - n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1]; - ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++; - } - else if (ArrayDescriptor.NT == 'D') { - double[] arow = HDFNativeData.byteToDouble(n, - ArrayDescriptor.dimlen[ArrayDescriptor.dims], - _barray); - java.lang.reflect.Array - .set( - ArrayDescriptor.objs[ArrayDescriptor.dims - 2], - (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]), - arow); - - n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1]; - ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++; - } - else if (ArrayDescriptor.NT == 'L') { - if (ArrayDescriptor.className.equals("java.lang.Byte")) { - Byte I[] = ByteToByteObj(n, - ArrayDescriptor.dimlen[ArrayDescriptor.dims], - _barray); - java.lang.reflect.Array - .set( - ArrayDescriptor.objs[ArrayDescriptor.dims - 2], - (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]), - I); - - n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1]; - ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++; - } - else if (ArrayDescriptor.className - .equals("java.lang.Integer")) { - Integer I[] = ByteToInteger(n, - ArrayDescriptor.dimlen[ArrayDescriptor.dims], - _barray); - java.lang.reflect.Array - .set( - ArrayDescriptor.objs[ArrayDescriptor.dims - 2], - (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]), - I); - - n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1]; - ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++; - } - else if (ArrayDescriptor.className - .equals("java.lang.Short")) { - Short I[] = ByteToShort(n, - ArrayDescriptor.dimlen[ArrayDescriptor.dims], - _barray); - java.lang.reflect.Array - .set( - ArrayDescriptor.objs[ArrayDescriptor.dims - 2], - (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]), - I); - - n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1]; - ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++; - } - else if (ArrayDescriptor.className - .equals("java.lang.Float")) { - Float I[] = ByteToFloatObj(n, - ArrayDescriptor.dimlen[ArrayDescriptor.dims], - _barray); - java.lang.reflect.Array - .set( - ArrayDescriptor.objs[ArrayDescriptor.dims - 2], - (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]), - I); - - n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1]; - ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++; - } - else if (ArrayDescriptor.className - .equals("java.lang.Double")) { - Double I[] = ByteToDoubleObj(n, - ArrayDescriptor.dimlen[ArrayDescriptor.dims], - _barray); - java.lang.reflect.Array - .set( - ArrayDescriptor.objs[ArrayDescriptor.dims - 2], - (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]), - I); - - n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1]; - ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++; - } - else if (ArrayDescriptor.className.equals("java.lang.Long")) { - Long I[] = ByteToLongObj(n, - ArrayDescriptor.dimlen[ArrayDescriptor.dims], - _barray); - java.lang.reflect.Array - .set( - ArrayDescriptor.objs[ArrayDescriptor.dims - 2], - (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]), - I); - - n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1]; - ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++; - } - else { - HDF5JavaException ex = new HDF5JavaException( - "HDFArray: unsupported Object type: " - + ArrayDescriptor.NT); - throw (ex); - } - } - else { - HDF5JavaException ex = new HDF5JavaException( - "HDFArray: unknown or unsupported type: " - + ArrayDescriptor.NT); - throw (ex); - } + Object arow = null; + int mm = m + ArrayDescriptor.dimlen[ArrayDescriptor.dims]; + switch (ArrayDescriptor.NT) { + case 'B': + arow = (Object) Arrays.copyOfRange((byte[]) flattenedArray, m, mm); + break; + case 'S': + arow = (Object) Arrays.copyOfRange((short[]) flattenedArray, m, mm); + break; + case 'I': + arow = (Object) Arrays.copyOfRange((int[]) flattenedArray, m, mm); + break; + case 'J': + arow = (Object) Arrays.copyOfRange((long[]) flattenedArray, m, mm); + break; + case 'F': + arow = (Object) Arrays.copyOfRange((float[]) flattenedArray, m, mm); + break; + case 'D': + arow = (Object) Arrays.copyOfRange((double[]) flattenedArray, m, mm); + break; + case 'L': + { + if (ArrayDescriptor.className.equals("java.lang.Byte")) + arow = (Object) Arrays.copyOfRange((Byte[]) flattenedArray, m, mm); + else if (ArrayDescriptor.className.equals("java.lang.Short")) + arow = (Object) Arrays.copyOfRange((Short[]) flattenedArray, m, mm); + else if (ArrayDescriptor.className.equals("java.lang.Integer")) + arow = (Object) Arrays.copyOfRange((Integer[]) flattenedArray, m, mm); + else if (ArrayDescriptor.className.equals("java.lang.Long")) + arow = (Object) Arrays.copyOfRange((Long[]) flattenedArray, m, mm); + else if (ArrayDescriptor.className.equals("java.lang.Float")) + arow = (Object) Arrays.copyOfRange((Float[]) flattenedArray, m, mm); + else if (ArrayDescriptor.className.equals("java.lang.Double")) + arow = (Object) Arrays.copyOfRange((Double[]) flattenedArray, m, mm); + else { + HDF5JavaException ex = new HDF5JavaException("HDFArray: unsupported Object type: " + ArrayDescriptor.NT); + throw (ex); + } + } // end of statement for arrays of boxed numerics + } // end of switch statement for arrays of primitives + + java.lang.reflect.Array.set(ArrayDescriptor.objs[ArrayDescriptor.dims - 2], + (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]), arow); + n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1]; + ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++; + m = mm; } catch (OutOfMemoryError err) { - HDF5JavaException ex = new HDF5JavaException( - "HDFArray: arrayify array too big?"); + HDF5JavaException ex = new HDF5JavaException("HDFArray: arrayify array too big?"); throw (ex); } - } /* assert: the whole array is completed--currentindex should == len - 1 */ - /* error checks */ - if (n < ArrayDescriptor.totalSize) { - throw new java.lang.InternalError(new String( - "HDFArray::arrayify Panic didn't complete all input data: n= " - + n + " size = " + ArrayDescriptor.totalSize)); + throw new java.lang.InternalError(new String("HDFArray::arrayify Panic didn't complete all input data: n= " + + n + " size = " + ArrayDescriptor.totalSize)); } for (i = 0; i <= ArrayDescriptor.dims - 2; i++) { if (ArrayDescriptor.currentindex[i] != ArrayDescriptor.dimlen[i] - 1) { - throw new java.lang.InternalError(new String( - "HDFArray::arrayify Panic didn't complete all data: currentindex[" - + i + "] = " + ArrayDescriptor.currentindex[i] - + " (should be " - + (ArrayDescriptor.dimlen[i] - 1) + "?")); - } - } - if (ArrayDescriptor.NT != 'B') { - if (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1] != ArrayDescriptor.dimlen[ArrayDescriptor.dims - 1]) { - throw new java.lang.InternalError(new String( - "HDFArray::arrayify Panic didn't complete all data: currentindex[" - + i + "] = " + ArrayDescriptor.currentindex[i] - + " (should be " + (ArrayDescriptor.dimlen[i]) + throw new java.lang.InternalError( + new String("HDFArray::arrayify Panic didn't complete all data: currentindex[" + i + "] = " + + ArrayDescriptor.currentindex[i] + " (should be " + (ArrayDescriptor.dimlen[i] - 1) + "?")); } } - else { - if (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1] != (ArrayDescriptor.dimlen[ArrayDescriptor.dims - 1] - 1)) { - throw new java.lang.InternalError(new String( - "HDFArray::arrayify Panic didn't complete all data: currentindex[" - + i + "] = " + ArrayDescriptor.currentindex[i] - + " (should be " - + (ArrayDescriptor.dimlen[i] - 1) + "?")); - } + if (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1] != ArrayDescriptor.dimlen[ArrayDescriptor.dims + - 1]) { + throw new java.lang.InternalError( + new String("HDFArray::arrayify Panic didn't complete all data: currentindex[" + i + "] = " + + ArrayDescriptor.currentindex[i] + " (should be " + (ArrayDescriptor.dimlen[i]) + "?")); } return _theArray; } - private byte[] IntegerToByte(Integer in[]) { + private byte[] IntegerToByte(Integer in[]) + { int nelems = java.lang.reflect.Array.getLength(in); int[] out = new int[nelems]; @@ -749,7 +573,8 @@ public class HDFArray { return HDFNativeData.intToByte(0, nelems, out); } - private Integer[] ByteToInteger(byte[] bin) { + private Integer[] ByteToInteger(byte[] bin) + { int in[] = HDFNativeData.byteToInt(bin); int nelems = java.lang.reflect.Array.getLength(in); Integer[] out = new Integer[nelems]; @@ -760,7 +585,8 @@ public class HDFArray { return out; } - private Integer[] ByteToInteger(int start, int len, byte[] bin) { + private Integer[] ByteToInteger(int start, int len, byte[] bin) + { int in[] = HDFNativeData.byteToInt(start, len, bin); int nelems = java.lang.reflect.Array.getLength(in); Integer[] out = new Integer[nelems]; @@ -771,7 +597,8 @@ public class HDFArray { return out; } - private byte[] ShortToByte(Short in[]) { + private byte[] ShortToByte(Short in[]) + { int nelems = java.lang.reflect.Array.getLength(in); short[] out = new short[nelems]; @@ -781,7 +608,8 @@ public class HDFArray { return HDFNativeData.shortToByte(0, nelems, out); } - private Short[] ByteToShort(byte[] bin) { + private Short[] ByteToShort(byte[] bin) + { short in[] = HDFNativeData.byteToShort(bin); int nelems = java.lang.reflect.Array.getLength((Object) in); Short[] out = new Short[nelems]; @@ -792,7 +620,8 @@ public class HDFArray { return out; } - private Short[] ByteToShort(int start, int len, byte[] bin) { + private Short[] ByteToShort(int start, int len, byte[] bin) + { short in[] = (short[]) HDFNativeData.byteToShort(start, len, bin); int nelems = java.lang.reflect.Array.getLength((Object) in); Short[] out = new Short[nelems]; @@ -803,7 +632,8 @@ public class HDFArray { return out; } - private byte[] ByteObjToByte(Byte in[]) { + private byte[] ByteObjToByte(Byte in[]) + { int nelems = java.lang.reflect.Array.getLength((Object) in); byte[] out = new byte[nelems]; @@ -813,7 +643,8 @@ public class HDFArray { return out; } - private Byte[] ByteToByteObj(byte[] bin) { + private Byte[] ByteToByteObj(byte[] bin) + { int nelems = java.lang.reflect.Array.getLength((Object) bin); Byte[] out = new Byte[nelems]; @@ -823,7 +654,8 @@ public class HDFArray { return out; } - private Byte[] ByteToByteObj(int start, int len, byte[] bin) { + private Byte[] ByteToByteObj(int start, int len, byte[] bin) + { Byte[] out = new Byte[len]; for (int i = 0; i < len; i++) { @@ -832,7 +664,8 @@ public class HDFArray { return out; } - private byte[] FloatObjToByte(Float in[]) { + private byte[] FloatObjToByte(Float in[]) + { int nelems = java.lang.reflect.Array.getLength((Object) in); float[] out = new float[nelems]; @@ -842,7 +675,8 @@ public class HDFArray { return HDFNativeData.floatToByte(0, nelems, out); } - private Float[] ByteToFloatObj(byte[] bin) { + private Float[] ByteToFloatObj(byte[] bin) + { float in[] = (float[]) HDFNativeData.byteToFloat(bin); int nelems = java.lang.reflect.Array.getLength((Object) in); Float[] out = new Float[nelems]; @@ -853,7 +687,8 @@ public class HDFArray { return out; } - private Float[] ByteToFloatObj(int start, int len, byte[] bin) { + private Float[] ByteToFloatObj(int start, int len, byte[] bin) + { float in[] = (float[]) HDFNativeData.byteToFloat(start, len, bin); int nelems = java.lang.reflect.Array.getLength((Object) in); Float[] out = new Float[nelems]; @@ -864,7 +699,8 @@ public class HDFArray { return out; } - private byte[] DoubleObjToByte(Double in[]) { + private byte[] DoubleObjToByte(Double in[]) + { int nelems = java.lang.reflect.Array.getLength((Object) in); double[] out = new double[nelems]; @@ -874,7 +710,8 @@ public class HDFArray { return HDFNativeData.doubleToByte(0, nelems, out); } - private Double[] ByteToDoubleObj(byte[] bin) { + private Double[] ByteToDoubleObj(byte[] bin) + { double in[] = (double[]) HDFNativeData.byteToDouble(bin); int nelems = java.lang.reflect.Array.getLength((Object) in); Double[] out = new Double[nelems]; @@ -885,7 +722,8 @@ public class HDFArray { return out; } - private Double[] ByteToDoubleObj(int start, int len, byte[] bin) { + private Double[] ByteToDoubleObj(int start, int len, byte[] bin) + { double in[] = (double[]) HDFNativeData.byteToDouble(start, len, bin); int nelems = java.lang.reflect.Array.getLength((Object) in); Double[] out = new Double[nelems]; @@ -896,7 +734,8 @@ public class HDFArray { return out; } - private byte[] LongObjToByte(Long in[]) { + private byte[] LongObjToByte(Long in[]) + { int nelems = java.lang.reflect.Array.getLength((Object) in); long[] out = new long[nelems]; @@ -906,7 +745,8 @@ public class HDFArray { return HDFNativeData.longToByte(0, nelems, out); } - private Long[] ByteToLongObj(byte[] bin) { + private Long[] ByteToLongObj(byte[] bin) + { long in[] = (long[]) HDFNativeData.byteToLong(bin); int nelems = java.lang.reflect.Array.getLength((Object) in); Long[] out = new Long[nelems]; @@ -917,7 +757,8 @@ public class HDFArray { return out; } - private Long[] ByteToLongObj(int start, int len, byte[] bin) { + private Long[] ByteToLongObj(int start, int len, byte[] bin) + { long in[] = (long[]) HDFNativeData.byteToLong(start, len, bin); int nelems = java.lang.reflect.Array.getLength((Object) in); Long[] out = new Long[nelems]; @@ -930,13 +771,11 @@ public class HDFArray { } /** - * This private class is used by HDFArray to discover the shape and type of an - * arbitrary array. + * This private class is used by HDFArray to discover the shape and type of an arbitrary array. * <p> * We use java.lang.reflection here. */ class ArrayDescriptor { - static String theType = ""; static Class theClass = null; static int[] dimlen = null; @@ -944,19 +783,19 @@ class ArrayDescriptor { static int[] currentindex = null; static int[] bytetoindex = null; static int totalSize = 0; + static int totalElements = 0; static Object[] objs = null; static char NT = ' '; /* must be B,S,I,L,F,D, else error */ static int NTsize = 0; static int dims = 0; static String className; - public ArrayDescriptor(Object anArray) throws HDF5Exception { - + public ArrayDescriptor(Object anArray) throws HDF5Exception + { Class tc = anArray.getClass(); if (tc.isArray() == false) { /* exception: not an array */ - HDF5Exception ex = new HDF5JavaException( - "ArrayDescriptor: not an array?: "); + HDF5Exception ex = new HDF5JavaException("ArrayDescriptor: not an array?: "); throw (ex); } @@ -1028,16 +867,14 @@ class ArrayDescriptor { NT = 'L'; className = "java.lang.String"; NTsize = 1; - throw new HDF5JavaException(new String( - "ArrayDesciptor: Warning: String array not fully supported yet")); + throw new HDF5JavaException(new String("ArrayDesciptor: Warning: String array not fully supported yet")); } else { /* * exception: not a numeric type */ - throw new HDF5JavaException(new String( - "ArrayDesciptor: Error: array is not numeric (type is " - + css + ") ?")); + throw new HDF5JavaException( + new String("ArrayDesciptor: Error: array is not numeric (type is " + css + ") ?")); } /* fill in the table */ @@ -1052,6 +889,7 @@ class ArrayDescriptor { dimlen[0] = 1; dimstart[0] = 0; currentindex[0] = 0; + int elements = 1; int i; for (i = 1; i <= dims; i++) { dimlen[i] = java.lang.reflect.Array.getLength((Object) o); @@ -1059,7 +897,9 @@ class ArrayDescriptor { objs[i] = o; dimstart[i] = 0; currentindex[i] = 0; + elements *= dimlen[i]; } + totalElements = elements; int j; int dd; @@ -1078,20 +918,19 @@ class ArrayDescriptor { /** * Debug dump */ - public void dumpInfo() { + public void dumpInfo() + { System.out.println("Type: " + theType); System.out.println("Class: " + theClass); System.out.println("NT: " + NT + " NTsize: " + NTsize); System.out.println("Array has " + dims + " dimensions (" + totalSize - + " bytes)"); + + " bytes, " + totalElements + " elements)"); int i; for (i = 0; i <= dims; i++) { Class tc = objs[i].getClass(); String ss = tc.toString(); - System.out.println(i + ": start " + dimstart[i] + ": len " - + dimlen[i] + " current " + currentindex[i] - + " bytetoindex " + bytetoindex[i] + " object " + objs[i] - + " otype " + ss); + System.out.println(i + ": start " + dimstart[i] + ": len " + dimlen[i] + " current " + currentindex[i] + + " bytetoindex " + bytetoindex[i] + " object " + objs[i] + " otype " + ss); } } } diff --git a/java/src/hdf/hdf5lib/HDFNativeData.java b/java/src/hdf/hdf5lib/HDFNativeData.java index 9637f62..5b29050 100644 --- a/java/src/hdf/hdf5lib/HDFNativeData.java +++ b/java/src/hdf/hdf5lib/HDFNativeData.java @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/hdf/hdf5lib/callbacks/Callbacks.java b/java/src/hdf/hdf5lib/callbacks/Callbacks.java index 9fc961a..11fa465 100644 --- a/java/src/hdf/hdf5lib/callbacks/Callbacks.java +++ b/java/src/hdf/hdf5lib/callbacks/Callbacks.java @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/hdf/hdf5lib/callbacks/H5A_iterate_cb.java b/java/src/hdf/hdf5lib/callbacks/H5A_iterate_cb.java index 988c8fb..6c68f36 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5A_iterate_cb.java +++ b/java/src/hdf/hdf5lib/callbacks/H5A_iterate_cb.java @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -15,7 +14,28 @@ package hdf.hdf5lib.callbacks; import hdf.hdf5lib.structs.H5A_info_t; -//Information class for link callback(for H5Aiterate) +/** + * Information class for link callback for H5Aiterate. + * + */ public interface H5A_iterate_cb extends Callbacks { - int callback(long group, String name, H5A_info_t info, H5A_iterate_t op_data); + /** + * application callback for each attribute + * + * @param loc_id the ID for the group or dataset being iterated over + * @param name the name of the current attribute about the object + * @param info the attribute's "info" struct + * @param op_data the operator data passed in to H5Aiterate + * + * @return operation status + * A. Zero causes the iterator to continue, returning zero when all + * attributes have been processed. + * B. Positive causes the iterator to immediately return that positive + * value, indicating short-circuit success. The iterator can be + * restarted at the next attribute. + * C. Negative causes the iterator to immediately return that value, + * indicating failure. The iterator can be restarted at the next + * attribute. + */ + int callback(long loc_id, String name, H5A_info_t info, H5A_iterate_t op_data); } diff --git a/java/src/hdf/hdf5lib/callbacks/H5A_iterate_t.java b/java/src/hdf/hdf5lib/callbacks/H5A_iterate_t.java index 51d67d5..d612db3 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5A_iterate_t.java +++ b/java/src/hdf/hdf5lib/callbacks/H5A_iterate_t.java @@ -1,18 +1,21 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package hdf.hdf5lib.callbacks; +/** + * Data class for link callback for H5Aiterate. + * + */ public interface H5A_iterate_t { /** public ArrayList iterdata = new ArrayList(); * Any derived interfaces must define the single public variable as above. diff --git a/java/src/hdf/hdf5lib/callbacks/H5D_append_cb.java b/java/src/hdf/hdf5lib/callbacks/H5D_append_cb.java index ead8f73..cf7ada6 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5D_append_cb.java +++ b/java/src/hdf/hdf5lib/callbacks/H5D_append_cb.java @@ -1,19 +1,38 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package hdf.hdf5lib.callbacks; -//Information class for link callback(for H5Pset/get_append_flush) +/** + * Information class for link callback for H5Pset/get_append_flush. + * + */ public interface H5D_append_cb extends Callbacks { + /** + * application callback for each dataset access property list + * + * @param dataset_id the ID for the dataset being iterated over + * @param cur_dims the dimension sizes for determining boundary + * @param op_data the operator data passed in to H5Pset/get_append_flush + * + * @return operation status + * A. Zero causes the iterator to continue, returning zero when all + * attributes have been processed. + * B. Positive causes the iterator to immediately return that positive + * value, indicating short-circuit success. The iterator can be + * restarted at the next attribute. + * C. Negative causes the iterator to immediately return that value, + * indicating failure. The iterator can be restarted at the next + * attribute. + */ int callback(long dataset_id, long[] cur_dims, H5D_append_t op_data); } diff --git a/java/src/hdf/hdf5lib/callbacks/H5D_append_t.java b/java/src/hdf/hdf5lib/callbacks/H5D_append_t.java index 8bf6410..7fdb454 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5D_append_t.java +++ b/java/src/hdf/hdf5lib/callbacks/H5D_append_t.java @@ -1,18 +1,21 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package hdf.hdf5lib.callbacks; +/** + * Data class for link callback for H5Dappend. + * + */ public interface H5D_append_t { /** public ArrayList iterdata = new ArrayList(); * Any derived interfaces must define the single public variable as above. diff --git a/java/src/hdf/hdf5lib/callbacks/H5D_iterate_cb.java b/java/src/hdf/hdf5lib/callbacks/H5D_iterate_cb.java index a911a1c..54c12e3 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5D_iterate_cb.java +++ b/java/src/hdf/hdf5lib/callbacks/H5D_iterate_cb.java @@ -1,19 +1,40 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package hdf.hdf5lib.callbacks; -//Information class for link callback(for H5Diterate) +/** + * Information class for link callback for H5Diterate. + * + */ public interface H5D_iterate_cb extends Callbacks { + /** + * application callback for each dataset element + * + * @param elem the pointer to the element in memory containing the current point + * @param elem_type the datatype ID for the elements stored in elem + * @param ndim the number of dimensions for POINT array + * @param point the array containing the location of the element within the original dataspace + * @param op_data the operator data passed in to H5Diterate + * + * @return operation status + * A. Zero causes the iterator to continue, returning zero when all + * attributes have been processed. + * B. Positive causes the iterator to immediately return that positive + * value, indicating short-circuit success. The iterator can be + * restarted at the next attribute. + * C. Negative causes the iterator to immediately return that value, + * indicating failure. The iterator can be restarted at the next + * attribute. + */ int callback(byte[] elem, long elem_type, int ndim, long[] point, H5D_iterate_t op_data); } diff --git a/java/src/hdf/hdf5lib/callbacks/H5D_iterate_t.java b/java/src/hdf/hdf5lib/callbacks/H5D_iterate_t.java index d049711..305cf98 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5D_iterate_t.java +++ b/java/src/hdf/hdf5lib/callbacks/H5D_iterate_t.java @@ -1,18 +1,21 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package hdf.hdf5lib.callbacks; +/** + * Data class for link callback for H5Diterate. + * + */ public interface H5D_iterate_t { /** public ArrayList iterdata = new ArrayList(); * Any derived interfaces must define the single public variable as above. diff --git a/java/src/hdf/hdf5lib/callbacks/H5E_walk_cb.java b/java/src/hdf/hdf5lib/callbacks/H5E_walk_cb.java index afc04ae..5722195 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5E_walk_cb.java +++ b/java/src/hdf/hdf5lib/callbacks/H5E_walk_cb.java @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -15,7 +14,27 @@ package hdf.hdf5lib.callbacks; import hdf.hdf5lib.structs.H5E_error2_t; -//Information class for link callback(for H5Ewalk) +/** + * Information class for link callback for H5Ewalk. + * + */ public interface H5E_walk_cb extends Callbacks { + /** + * application callback for each error stack element + * + * @param nidx the index of the current error stack element + * @param info the error stack "info" struct + * @param op_data the operator data passed in to H5Ewalk + * + * @return operation status + * A. Zero causes the iterator to continue, returning zero when all + * attributes have been processed. + * B. Positive causes the iterator to immediately return that positive + * value, indicating short-circuit success. The iterator can be + * restarted at the next attribute. + * C. Negative causes the iterator to immediately return that value, + * indicating failure. The iterator can be restarted at the next + * attribute. + */ int callback(int nidx, H5E_error2_t info, H5E_walk_t op_data); } diff --git a/java/src/hdf/hdf5lib/callbacks/H5E_walk_t.java b/java/src/hdf/hdf5lib/callbacks/H5E_walk_t.java index 0be8977..5bf0c8b 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5E_walk_t.java +++ b/java/src/hdf/hdf5lib/callbacks/H5E_walk_t.java @@ -1,18 +1,21 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package hdf.hdf5lib.callbacks; +/** + * Data class for link callback for H5Ewalk. + * + */ public interface H5E_walk_t { /** public ArrayList iterdata = new ArrayList(); * Any derived interfaces must define the single public variable as above. diff --git a/java/src/hdf/hdf5lib/callbacks/H5L_iterate_opdata_t.java b/java/src/hdf/hdf5lib/callbacks/H5L_iterate_opdata_t.java index ad9ad8c..d89fd2a 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5L_iterate_opdata_t.java +++ b/java/src/hdf/hdf5lib/callbacks/H5L_iterate_opdata_t.java @@ -1,18 +1,21 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package hdf.hdf5lib.callbacks; +/** + * Data class for link callback for H5Lvisit/H5Lvisit_by_name. + * + */ public interface H5L_iterate_opdata_t { } diff --git a/java/src/hdf/hdf5lib/callbacks/H5L_iterate_t.java b/java/src/hdf/hdf5lib/callbacks/H5L_iterate_t.java index f92fbc4..53635bf 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5L_iterate_t.java +++ b/java/src/hdf/hdf5lib/callbacks/H5L_iterate_t.java @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -15,7 +14,28 @@ package hdf.hdf5lib.callbacks; import hdf.hdf5lib.structs.H5L_info_t; -// Information class for link callback (for H5Lvisit/H5Lvisit_by_name). +/** + * Information class for link callback for H5Lvisit/H5Lvisit_by_name. + * + */ public interface H5L_iterate_t extends Callbacks { - int callback(long group, String name, H5L_info_t info, H5L_iterate_opdata_t op_data); + /** + * application callback for each group + * + * @param loc_id the ID for the group being iterated over + * @param name the name of the current link + * @param info the link's "info" struct + * @param op_data the operator data passed in to H5Literate + * + * @return operation status + * A. Zero causes the iterator to continue, returning zero when all + * attributes have been processed. + * B. Positive causes the iterator to immediately return that positive + * value, indicating short-circuit success. The iterator can be + * restarted at the next attribute. + * C. Negative causes the iterator to immediately return that value, + * indicating failure. The iterator can be restarted at the next + * attribute. + */ + int callback(long loc_id, String name, H5L_info_t info, H5L_iterate_opdata_t op_data); } diff --git a/java/src/hdf/hdf5lib/callbacks/H5O_iterate_opdata_t.java b/java/src/hdf/hdf5lib/callbacks/H5O_iterate_opdata_t.java index e1c47b5..fd643b4 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5O_iterate_opdata_t.java +++ b/java/src/hdf/hdf5lib/callbacks/H5O_iterate_opdata_t.java @@ -1,18 +1,21 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package hdf.hdf5lib.callbacks; +/** + * Data class for link callback for H5Ovisit/H5Ovisit_by_name. + * + */ public interface H5O_iterate_opdata_t { } diff --git a/java/src/hdf/hdf5lib/callbacks/H5O_iterate_t.java b/java/src/hdf/hdf5lib/callbacks/H5O_iterate_t.java index 9a55106..ecf868c 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5O_iterate_t.java +++ b/java/src/hdf/hdf5lib/callbacks/H5O_iterate_t.java @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -15,7 +14,28 @@ package hdf.hdf5lib.callbacks; import hdf.hdf5lib.structs.H5O_info_t; -// Information class for link callback(for H5Ovisit/H5Ovisit_by_name) +/** + * Information class for link callback for H5Ovisit/H5Ovisit_by_name. + * + */ public interface H5O_iterate_t extends Callbacks { - int callback(long group, String name, H5O_info_t info, H5O_iterate_opdata_t op_data); + /** + * application callback for each group + * + * @param loc_id the ID for the group or dataset being iterated over + * @param name the name of the current object + * @param info the object's "info" struct + * @param op_data the operator data passed in to H5Oiterate + * + * @return operation status + * A. Zero causes the iterator to continue, returning zero when all + * attributes have been processed. + * B. Positive causes the iterator to immediately return that positive + * value, indicating short-circuit success. The iterator can be + * restarted at the next attribute. + * C. Negative causes the iterator to immediately return that value, + * indicating failure. The iterator can be restarted at the next + * attribute. + */ + int callback(long loc_id, String name, H5O_info_t info, H5O_iterate_opdata_t op_data); } diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_cls_close_func_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_cls_close_func_cb.java index e77d386..0a09a94 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5P_cls_close_func_cb.java +++ b/java/src/hdf/hdf5lib/callbacks/H5P_cls_close_func_cb.java @@ -1,19 +1,37 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package hdf.hdf5lib.callbacks; -//Information class for link callback(for H5Pcreate_class) +/** + * Information class for link callback for H5Pcreate_class. + * + */ public interface H5P_cls_close_func_cb extends Callbacks { + /** + * application callback for each property list + * + * @param prop_id the ID for the property list class being iterated over + * @param close_data the function to call when a property list is closed + * + * @return operation status + * A. Zero causes the iterator to continue, returning zero when all + * attributes have been processed. + * B. Positive causes the iterator to immediately return that positive + * value, indicating short-circuit success. The iterator can be + * restarted at the next attribute. + * C. Negative causes the iterator to immediately return that value, + * indicating failure. The iterator can be restarted at the next + * attribute. + */ int callback(long prop_id, H5P_cls_close_func_t close_data); } diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_cls_close_func_t.java b/java/src/hdf/hdf5lib/callbacks/H5P_cls_close_func_t.java index 0d5ad9e..11e3a99 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5P_cls_close_func_t.java +++ b/java/src/hdf/hdf5lib/callbacks/H5P_cls_close_func_t.java @@ -1,18 +1,21 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package hdf.hdf5lib.callbacks; +/** + * Data class for link callback for H5Pcreate_class. + * + */ public interface H5P_cls_close_func_t { /** public ArrayList iterdata = new ArrayList(); * Any derived interfaces must define the single public variable as above. diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_cls_copy_func_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_cls_copy_func_cb.java index 139f877..53f86be 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5P_cls_copy_func_cb.java +++ b/java/src/hdf/hdf5lib/callbacks/H5P_cls_copy_func_cb.java @@ -1,19 +1,38 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package hdf.hdf5lib.callbacks; -//Information class for link callback(for H5Pcreate_class) +/** + * Information class for link callback for H5Pcreate_class + * + */ public interface H5P_cls_copy_func_cb extends Callbacks { + /** + * application callback for each property list + * + * @param new_prop_id the ID for the property list copy + * @param old_prop_id the ID for the property list class being copied + * @param copy_data the function to call when each property list in this class is copied + * + * @return operation status + * A. Zero causes the iterator to continue, returning zero when all + * attributes have been processed. + * B. Positive causes the iterator to immediately return that positive + * value, indicating short-circuit success. The iterator can be + * restarted at the next attribute. + * C. Negative causes the iterator to immediately return that value, + * indicating failure. The iterator can be restarted at the next + * attribute. + */ int callback(long new_prop_id, long old_prop_id, H5P_cls_copy_func_t copy_data); } diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_cls_copy_func_t.java b/java/src/hdf/hdf5lib/callbacks/H5P_cls_copy_func_t.java index 12c2601..78e5282 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5P_cls_copy_func_t.java +++ b/java/src/hdf/hdf5lib/callbacks/H5P_cls_copy_func_t.java @@ -1,18 +1,21 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package hdf.hdf5lib.callbacks; +/** + * Data class for link callback for H5Pcreate_class. + * + */ public interface H5P_cls_copy_func_t { /** public ArrayList iterdata = new ArrayList(); * Any derived interfaces must define the single public variable as above. diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_cls_create_func_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_cls_create_func_cb.java index e64ec6f..8f4e782 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5P_cls_create_func_cb.java +++ b/java/src/hdf/hdf5lib/callbacks/H5P_cls_create_func_cb.java @@ -1,19 +1,37 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package hdf.hdf5lib.callbacks; -//Information class for link callback(for H5Pcreate_class) +/** + * Information class for link callback for H5Pcreate_class. + * + */ public interface H5P_cls_create_func_cb extends Callbacks { + /** + * application callback for each property list + * + * @param prop_id the ID for the property list class being iterated over + * @param create_data the function to call when each property list in this class is created + * + * @return operation status + * A. Zero causes the iterator to continue, returning zero when all + * attributes have been processed. + * B. Positive causes the iterator to immediately return that positive + * value, indicating short-circuit success. The iterator can be + * restarted at the next attribute. + * C. Negative causes the iterator to immediately return that value, + * indicating failure. The iterator can be restarted at the next + * attribute. + */ int callback(long prop_id, H5P_cls_create_func_t create_data); } diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_cls_create_func_t.java b/java/src/hdf/hdf5lib/callbacks/H5P_cls_create_func_t.java index 73646f1..d919d97 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5P_cls_create_func_t.java +++ b/java/src/hdf/hdf5lib/callbacks/H5P_cls_create_func_t.java @@ -1,18 +1,21 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package hdf.hdf5lib.callbacks; +/** + * Data class for link callback for H5Pcreate_class. + * + */ public interface H5P_cls_create_func_t { /** public ArrayList iterdata = new ArrayList(); * Any derived interfaces must define the single public variable as above. diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_iterate_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_iterate_cb.java index 5ecb88d..db98a67 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5P_iterate_cb.java +++ b/java/src/hdf/hdf5lib/callbacks/H5P_iterate_cb.java @@ -1,19 +1,38 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package hdf.hdf5lib.callbacks; -//Information class for link callback(for H5Piterate) +/** + * Information class for link callback for H5Piterate. + * + */ public interface H5P_iterate_cb extends Callbacks { + /** + * application callback for each property list + * + * @param plist the ID for the property list being iterated over + * @param name the name of the current property list + * @param op_data the operator data passed in to H5Piterate + * + * @return operation status + * A. Zero causes the iterator to continue, returning zero when all + * attributes have been processed. + * B. Positive causes the iterator to immediately return that positive + * value, indicating short-circuit success. The iterator can be + * restarted at the next attribute. + * C. Negative causes the iterator to immediately return that value, + * indicating failure. The iterator can be restarted at the next + * attribute. + */ int callback(long plist, String name, H5P_iterate_t op_data); } diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_iterate_t.java b/java/src/hdf/hdf5lib/callbacks/H5P_iterate_t.java index 2e320b4..0035619 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5P_iterate_t.java +++ b/java/src/hdf/hdf5lib/callbacks/H5P_iterate_t.java @@ -1,18 +1,21 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package hdf.hdf5lib.callbacks; +/** + * Data class for link callback for H5Piterate. + * + */ public interface H5P_iterate_t { /** public ArrayList iterdata = new ArrayList(); * Any derived interfaces must define the single public variable as above. diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_prp_close_func_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_prp_close_func_cb.java index 103fe5f..1aa7ce4 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5P_prp_close_func_cb.java +++ b/java/src/hdf/hdf5lib/callbacks/H5P_prp_close_func_cb.java @@ -1,19 +1,38 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package hdf.hdf5lib.callbacks; -//Information class for link callback(for H5Pregister2) +/** + * Information class for link callback for H5Pregister2. + * + */ public interface H5P_prp_close_func_cb extends Callbacks { + /** + * application callback for each property list + * + * @param name the name of the property being closed + * @param size the size of the property value + * @param value the value of the property being closed + * + * @return operation status + * A. Zero causes the iterator to continue, returning zero when all + * attributes have been processed. + * B. Positive causes the iterator to immediately return that positive + * value, indicating short-circuit success. The iterator can be + * restarted at the next attribute. + * C. Negative causes the iterator to immediately return that value, + * indicating failure. The iterator can be restarted at the next + * attribute. + */ int callback(String name, long size, byte[] value); } diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_prp_compare_func_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_prp_compare_func_cb.java index 46477b9..49cef7d 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5P_prp_compare_func_cb.java +++ b/java/src/hdf/hdf5lib/callbacks/H5P_prp_compare_func_cb.java @@ -1,19 +1,38 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package hdf.hdf5lib.callbacks; -//Information class for link callback(for H5Pregister2) +/** + * Information class for link callback for H5Pregister2. + * + */ public interface H5P_prp_compare_func_cb extends Callbacks { + /** + * application callback for each property list + * + * @param value1 the value of the first property being compared + * @param value2 the value of the second property being compared + * @param size the size of the property value + * + * @return operation status + * A. Zero causes the iterator to continue, returning zero when all + * attributes have been processed. + * B. Positive causes the iterator to immediately return that positive + * value, indicating short-circuit success. The iterator can be + * restarted at the next attribute. + * C. Negative causes the iterator to immediately return that value, + * indicating failure. The iterator can be restarted at the next + * attribute. + */ int callback(byte[] value1, byte[] value2, long size); } diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_prp_copy_func_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_prp_copy_func_cb.java index 57994bb5..f4924ee 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5P_prp_copy_func_cb.java +++ b/java/src/hdf/hdf5lib/callbacks/H5P_prp_copy_func_cb.java @@ -1,19 +1,38 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package hdf.hdf5lib.callbacks; -//Information class for link callback(for H5Pregister2) +/** + * Information class for link callback for H5Pregister2. + * + */ public interface H5P_prp_copy_func_cb extends Callbacks { + /** + * application callback for each property list + * + * @param name the name of the property being copied + * @param size the size of the property value + * @param value the value of the property being copied + * + * @return operation status + * A. Zero causes the iterator to continue, returning zero when all + * attributes have been processed. + * B. Positive causes the iterator to immediately return that positive + * value, indicating short-circuit success. The iterator can be + * restarted at the next attribute. + * C. Negative causes the iterator to immediately return that value, + * indicating failure. The iterator can be restarted at the next + * attribute. + */ int callback(String name, long size, byte[] value); } diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_prp_create_func_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_prp_create_func_cb.java index 8791c22..bce024b 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5P_prp_create_func_cb.java +++ b/java/src/hdf/hdf5lib/callbacks/H5P_prp_create_func_cb.java @@ -1,19 +1,38 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package hdf.hdf5lib.callbacks; -//Information class for link callback(for H5Pregister2) +/** + * Information class for link callback for H5Pregister2. + * + */ public interface H5P_prp_create_func_cb extends Callbacks { + /** + * application callback for each property list + * + * @param name the name of the property list being created + * @param size the size of the property value + * @param value the initial value for the property being created + * + * @return operation status + * A. Zero causes the iterator to continue, returning zero when all + * attributes have been processed. + * B. Positive causes the iterator to immediately return that positive + * value, indicating short-circuit success. The iterator can be + * restarted at the next attribute. + * C. Negative causes the iterator to immediately return that value, + * indicating failure. The iterator can be restarted at the next + * attribute. + */ int callback(String name, long size, byte[] value); } diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_prp_delete_func_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_prp_delete_func_cb.java index 46cd097..8c5dccc 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5P_prp_delete_func_cb.java +++ b/java/src/hdf/hdf5lib/callbacks/H5P_prp_delete_func_cb.java @@ -1,19 +1,39 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package hdf.hdf5lib.callbacks; -//Information class for link callback(for H5Pregister2) +/** + * Information class for link callback for H5Pregister2. + * + */ public interface H5P_prp_delete_func_cb extends Callbacks { + /** + * application callback for each property list + * + * @param prop_id the ID of the property list the property is deleted from + * @param name the name of the property being deleted + * @param size the size of the property value + * @param value the value of the property being deleted + * + * @return operation status + * A. Zero causes the iterator to continue, returning zero when all + * attributes have been processed. + * B. Positive causes the iterator to immediately return that positive + * value, indicating short-circuit success. The iterator can be + * restarted at the next attribute. + * C. Negative causes the iterator to immediately return that value, + * indicating failure. The iterator can be restarted at the next + * attribute. + */ int callback(long prop_id, String name, long size, byte[] value); } diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_prp_get_func_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_prp_get_func_cb.java index 04599a0..0f3457f 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5P_prp_get_func_cb.java +++ b/java/src/hdf/hdf5lib/callbacks/H5P_prp_get_func_cb.java @@ -1,19 +1,39 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package hdf.hdf5lib.callbacks; -//Information class for link callback(for H5Pregister2) +/** + * Information class for link callback for H5Pregister2. + * + */ public interface H5P_prp_get_func_cb extends Callbacks { + /** + * application callback for each property list + * + * @param prop_id the ID for the property list being queried + * @param name the name of the property being queried + * @param size the size of the property value + * @param value the value being retrieved for the property + * + * @return operation status + * A. Zero causes the iterator to continue, returning zero when all + * attributes have been processed. + * B. Positive causes the iterator to immediately return that positive + * value, indicating short-circuit success. The iterator can be + * restarted at the next attribute. + * C. Negative causes the iterator to immediately return that value, + * indicating failure. The iterator can be restarted at the next + * attribute. + */ int callback(long prop_id, String name, long size, byte[] value); } diff --git a/java/src/hdf/hdf5lib/callbacks/H5P_prp_set_func_cb.java b/java/src/hdf/hdf5lib/callbacks/H5P_prp_set_func_cb.java index 6ac750f..a55ca3a 100644 --- a/java/src/hdf/hdf5lib/callbacks/H5P_prp_set_func_cb.java +++ b/java/src/hdf/hdf5lib/callbacks/H5P_prp_set_func_cb.java @@ -1,19 +1,39 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package hdf.hdf5lib.callbacks; -//Information class for link callback(for H5Pregister2) +/** + * Information class for link callback for H5Pregister2. + * + */ public interface H5P_prp_set_func_cb extends Callbacks { + /** + * application callback for each property list + * + * @param prop_id the ID for the property list being modified + * @param name the name of the property being modified + * @param size the size of the property value + * @param value the value being set for the property + * + * @return operation status + * A. Zero causes the iterator to continue, returning zero when all + * attributes have been processed. + * B. Positive causes the iterator to immediately return that positive + * value, indicating short-circuit success. The iterator can be + * restarted at the next attribute. + * C. Negative causes the iterator to immediately return that value, + * indicating failure. The iterator can be restarted at the next + * attribute. + */ int callback(long prop_id, String name, long size, byte[] value); } diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5AtomException.java b/java/src/hdf/hdf5lib/exceptions/HDF5AtomException.java index 850044c..ee1b21f 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5AtomException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5AtomException.java @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5AttributeException.java b/java/src/hdf/hdf5lib/exceptions/HDF5AttributeException.java index 87b075b..86dad88 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5AttributeException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5AttributeException.java @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5BtreeException.java b/java/src/hdf/hdf5lib/exceptions/HDF5BtreeException.java index 5118254..97585d3 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5BtreeException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5BtreeException.java @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5DataFiltersException.java b/java/src/hdf/hdf5lib/exceptions/HDF5DataFiltersException.java index 14ae43f..b02d815 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5DataFiltersException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5DataFiltersException.java @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5DataStorageException.java b/java/src/hdf/hdf5lib/exceptions/HDF5DataStorageException.java index 721d3ef..416b06a 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5DataStorageException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5DataStorageException.java @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5DatasetInterfaceException.java b/java/src/hdf/hdf5lib/exceptions/HDF5DatasetInterfaceException.java index 3c55a6b..7bb22fa 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5DatasetInterfaceException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5DatasetInterfaceException.java @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5DataspaceInterfaceException.java b/java/src/hdf/hdf5lib/exceptions/HDF5DataspaceInterfaceException.java index c0182ee..9a85ff0 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5DataspaceInterfaceException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5DataspaceInterfaceException.java @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5DatatypeInterfaceException.java b/java/src/hdf/hdf5lib/exceptions/HDF5DatatypeInterfaceException.java index 4da074b..45b0c55 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5DatatypeInterfaceException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5DatatypeInterfaceException.java @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5Exception.java b/java/src/hdf/hdf5lib/exceptions/HDF5Exception.java index 1e4b5fd..0c23af1 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5Exception.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5Exception.java @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -31,6 +31,9 @@ package hdf.hdf5lib.exceptions; * */ public class HDF5Exception extends RuntimeException { + /** + * the specified detail message of this exception + */ protected String detailMessage; /** diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5ExternalFileListException.java b/java/src/hdf/hdf5lib/exceptions/HDF5ExternalFileListException.java index 28f5437..73bf069 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5ExternalFileListException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5ExternalFileListException.java @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5FileInterfaceException.java b/java/src/hdf/hdf5lib/exceptions/HDF5FileInterfaceException.java index c8dbcea..ac82258 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5FileInterfaceException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5FileInterfaceException.java @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5FunctionArgumentException.java b/java/src/hdf/hdf5lib/exceptions/HDF5FunctionArgumentException.java index e7f20e0..c4fcf30 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5FunctionArgumentException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5FunctionArgumentException.java @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5FunctionEntryExitException.java b/java/src/hdf/hdf5lib/exceptions/HDF5FunctionEntryExitException.java index 26e836f..ee34b59 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5FunctionEntryExitException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5FunctionEntryExitException.java @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5HeapException.java b/java/src/hdf/hdf5lib/exceptions/HDF5HeapException.java index a32e2a1..1bb3251 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5HeapException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5HeapException.java @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5InternalErrorException.java b/java/src/hdf/hdf5lib/exceptions/HDF5InternalErrorException.java index 25ac572..810c126 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5InternalErrorException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5InternalErrorException.java @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5JavaException.java b/java/src/hdf/hdf5lib/exceptions/HDF5JavaException.java index 7c61194..35720da 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5JavaException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5JavaException.java @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5LibraryException.java b/java/src/hdf/hdf5lib/exceptions/HDF5LibraryException.java index 54acbdd..efe1fdf 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5LibraryException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5LibraryException.java @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -30,7 +30,9 @@ import hdf.hdf5lib.HDF5Constants; @SuppressWarnings("serial") public class HDF5LibraryException extends HDF5Exception { + /** major error number of the first error on the HDF5 library error stack. */ private final long majorErrorNumber; + /** minor error number of the first error on the HDF5 library error stack. */ private final long minorErrorNumber; /** diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5LowLevelIOException.java b/java/src/hdf/hdf5lib/exceptions/HDF5LowLevelIOException.java index 6d792c3..d61f4e9 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5LowLevelIOException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5LowLevelIOException.java @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5MetaDataCacheException.java b/java/src/hdf/hdf5lib/exceptions/HDF5MetaDataCacheException.java index 02f2d33..3b64b15 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5MetaDataCacheException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5MetaDataCacheException.java @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5ObjectHeaderException.java b/java/src/hdf/hdf5lib/exceptions/HDF5ObjectHeaderException.java index 2bb6861..b9f40f8 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5ObjectHeaderException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5ObjectHeaderException.java @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5PropertyListInterfaceException.java b/java/src/hdf/hdf5lib/exceptions/HDF5PropertyListInterfaceException.java index b1baaad..d2a20e0 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5PropertyListInterfaceException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5PropertyListInterfaceException.java @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5ReferenceException.java b/java/src/hdf/hdf5lib/exceptions/HDF5ReferenceException.java index ea4a89a..0701244 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5ReferenceException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5ReferenceException.java @@ -6,13 +6,19 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package hdf.hdf5lib.exceptions; +/** + * The class HDF5LibraryException returns errors raised by the HDF5 library. + * <p> + * This sub-class represents HDF-5 major error code <b>H5E_REFERENCE</b> + */ + public class HDF5ReferenceException extends HDF5LibraryException { /** * Constructs an <code>HDF5ReferenceException</code> with no specified diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5ResourceUnavailableException.java b/java/src/hdf/hdf5lib/exceptions/HDF5ResourceUnavailableException.java index fc92578..ad052b5 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5ResourceUnavailableException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5ResourceUnavailableException.java @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5SymbolTableException.java b/java/src/hdf/hdf5lib/exceptions/HDF5SymbolTableException.java index b90ce64..ba9150f 100644 --- a/java/src/hdf/hdf5lib/exceptions/HDF5SymbolTableException.java +++ b/java/src/hdf/hdf5lib/exceptions/HDF5SymbolTableException.java @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/hdf/hdf5lib/structs/H5AC_cache_config_t.java b/java/src/hdf/hdf5lib/structs/H5AC_cache_config_t.java index 20863dc..cf84532 100644 --- a/java/src/hdf/hdf5lib/structs/H5AC_cache_config_t.java +++ b/java/src/hdf/hdf5lib/structs/H5AC_cache_config_t.java @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -15,44 +14,276 @@ package hdf.hdf5lib.structs; import java.io.Serializable; -//Information struct for H5Pget_mdc_config/H5Pset_mdc_config +/** + * Information struct for H5Pget_mdc_config/H5Pset_mdc_config + * + */ public class H5AC_cache_config_t implements Serializable{ private static final long serialVersionUID = -6748085696476149972L; - // general configuration fields: + // general configuration fields + /** + * version: Integer field containing the version number of this version + * of the H5AC_cache_config_t structure. Any instance of + * H5AC_cache_config_t passed to the cache must have a known + * version number, or an error will be flagged. + */ public int version; + /** + * rpt_fcn_enabled: Boolean field used to enable and disable the default + * reporting function. This function is invoked every time the + * automatic cache resize code is run, and reports on its activities. + * + * This is a debugging function, and should normally be turned off. + */ public boolean rpt_fcn_enabled; + /** + * open_trace_file: Boolean field indicating whether the trace_file_name + * field should be used to open a trace file for the cache. + * + * *** DEPRECATED *** Use H5Fstart/stop logging functions instead + */ public boolean open_trace_file; + /** + * close_trace_file: Boolean field indicating whether the current trace + * file (if any) should be closed. + * + * *** DEPRECATED *** Use H5Fstart/stop logging functions instead + */ public boolean close_trace_file; + /** + * trace_file_name: Full path of the trace file to be opened if the + * open_trace_file field is TRUE. + * + * *** DEPRECATED *** Use H5Fstart/stop logging functions instead + */ public String trace_file_name; + /** + * evictions_enabled: Boolean field used to either report the current + * evictions enabled status of the cache, or to set the cache's + * evictions enabled status. + */ public boolean evictions_enabled; + /** + * set_initial_size: Boolean flag indicating whether the size of the + * initial size of the cache is to be set to the value given in + * the initial_size field. If set_initial_size is FALSE, the + * initial_size field is ignored. + */ public boolean set_initial_size; + /** + * initial_size: If enabled, this field contain the size the cache is + * to be set to upon receipt of this structure. Needless to say, + * initial_size must lie in the closed interval [min_size, max_size]. + */ public long initial_size; + /** + * min_clean_fraction: double in the range 0 to 1 indicating the fraction + * of the cache that is to be kept clean. This field is only used + * in parallel mode. Typical values are 0.1 to 0.5. + */ public double min_clean_fraction; + /** + * max_size: Maximum size to which the cache can be adjusted. The + * supplied value must fall in the closed interval + * [MIN_MAX_CACHE_SIZE, MAX_MAX_CACHE_SIZE]. Also, max_size must + * be greater than or equal to min_size. + */ public long max_size; + /** + * min_size: Minimum size to which the cache can be adjusted. The + * supplied value must fall in the closed interval + * [H5C__MIN_MAX_CACHE_SIZE, H5C__MAX_MAX_CACHE_SIZE]. Also, min_size + * must be less than or equal to max_size. + */ public long min_size; + /** + * epoch_length: Number of accesses on the cache over which to collect + * hit rate stats before running the automatic cache resize code, + * if it is enabled. + */ public long epoch_length; - // size increase control fields: - public int incr_mode; // H5C_cache_incr_mode + // size increase control fields + /** + * incr_mode: Instance of the H5C_cache_incr_mode enumerated type whose + * value indicates how we determine whether the cache size should be + * increased. At present there are two possible values. + */ + public int incr_mode; + /** + * lower_hr_threshold: Lower hit rate threshold. If the increment mode + * (incr_mode) is H5C_incr__threshold and the hit rate drops below the + * value supplied in this field in an epoch, increment the cache size by + * size_increment. Note that cache size may not be incremented above + * max_size, and that the increment may be further restricted by the + * max_increment field if it is enabled. + */ public double lower_hr_threshold; + /** + * increment: Double containing the multiplier used to derive the new + * cache size from the old if a cache size increment is triggered. + * The increment must be greater than 1.0, and should not exceed 2.0. + */ public double increment; + /** + * apply_max_increment: Boolean flag indicating whether the max_increment + * field should be used to limit the maximum cache size increment. + */ public boolean apply_max_increment; + /** + * max_increment: If enabled by the apply_max_increment field described + * above, this field contains the maximum number of bytes by which the + * cache size can be increased in a single re-size. + */ public long max_increment; - public int flash_incr_mode; // H5C_cache_flash_incr_mode + /** + * flash_incr_mode: Instance of the H5C_cache_flash_incr_mode enumerated + * type whose value indicates whether and by which algorithm we should + * make flash increases in the size of the cache to accommodate insertion + * of large entries and large increases in the size of a single entry. + */ + public int flash_incr_mode; + /** + * flash_multiple: Double containing the multiple described above in the + * H5C_flash_incr__add_space section of the discussion of the + * flash_incr_mode section. This field is ignored unless flash_incr_mode + * is H5C_flash_incr__add_space. + */ public double flash_multiple; + /** + * flash_threshold: Double containing the factor by which current max cache + * size is multiplied to obtain the size threshold for the add_space flash + * increment algorithm. The field is ignored unless flash_incr_mode is + * H5C_flash_incr__add_space. + */ public double flash_threshold; - // size decrease control fields: - public int decr_mode; // H5C_cache_decr_mode + // size decrease control fields + /** + * decr_mode: Instance of the H5C_cache_decr_mode enumerated type whose + * value indicates how we determine whether the cache size should be + * decreased. At present there are four possibilities. + */ + public int decr_mode; + /** + * upper_hr_threshold: Upper hit rate threshold. The use of this field + * varies according to the current decr_mode. + */ public double upper_hr_threshold; + /** + * decrement: This field is only used when the decr_mode is + * H5C_decr__threshold. + */ public double decrement; + /** + * apply_max_decrement: Boolean flag used to determine whether decrements + * in cache size are to be limited by the max_decrement field. + */ public boolean apply_max_decrement; + /** + * max_decrement: Maximum number of bytes by which the cache size can be + * decreased in a single re-size. Note that decrements may also be + * restricted by the min_size of the cache, and (in age out modes) by + * the empty_reserve field. + */ public long max_decrement; + /** + * epochs_before_eviction: Integer field used in H5C_decr__age_out and + * H5C_decr__age_out_with_threshold decrement modes. + */ public int epochs_before_eviction; + /** + * apply_empty_reserve: Boolean field controlling whether the empty_reserve + * field is to be used in computing the new cache size when the + * decr_mode is H5C_decr__age_out or H5C_decr__age_out_with_threshold. + */ public boolean apply_empty_reserve; + /** + * empty_reserve: To avoid a constant racheting down of cache size by small + * amounts in the H5C_decr__age_out and H5C_decr__age_out_with_threshold + * modes, this field allows one to require that any cache size + * reductions leave the specified fraction of unused space in the cache. + */ public double empty_reserve; - // parallel configuration fields: + // parallel configuration fields + /** + * dirty_bytes_threshold: Threshold of dirty byte creation used to + * synchronize updates between caches. + */ public long dirty_bytes_threshold; + /** + * metadata_write_strategy: Integer field containing a code indicating the + * desired metadata write strategy. + */ public int metadata_write_strategy; + /** H5AC_cache_config_t is a public structure intended for use in public APIs. + * At least in its initial incarnation, it is basically a copy of struct + * H5C_auto_size_ctl_t, minus the report_fcn field, and plus the + * dirty_bytes_threshold field. + * + * @param version: Integer field containing the version number of this version + * @param rpt_fcn_enabled: Boolean field used to enable and disable the default reporting function. + * @param open_trace_file: Boolean field indicating whether the trace_file_name + * field should be used to open a trace file for the cache. + * @param close_trace_file: Boolean field indicating whether the current trace + * file (if any) should be closed. + * @param trace_file_name: Full path of the trace file to be opened if the + * open_trace_file field is TRUE. + * @param evictions_enabled: Boolean field used to either report or set the current + * evictions enabled status of the cache. + * @param set_initial_size: Boolean flag indicating whether the size of the + * initial size of the cache is to be set to the value given in + * the initial_size field. + * @param initial_size: If enabled, this field contain the size the cache is + * to be set to upon receipt of this structure. + * @param min_clean_fraction: double in the range 0 to 1 indicating the fraction + * of the cache that is to be kept clean. + * @param max_size: Maximum size to which the cache can be adjusted. + * @param min_size: Minimum size to which the cache can be adjusted. + * @param epoch_length: Number of accesses on the cache over which to collect + * hit rate stats before running the automatic cache resize code. + * @param incr_mode: Instance of the H5C_cache_incr_mode enumerated type. + * @param lower_hr_threshold: Lower hit rate threshold. + * @param increment: Double containing the multiplier used to derive the new + * cache size from the old if a cache size increment is triggered. + * @param apply_max_increment: Boolean flag indicating whether the max_increment + * field should be used to limit the maximum cache size increment. + * @param max_increment: If enabled by the apply_max_increment field described + * above, this field contains the maximum number of bytes by which the + * cache size can be increased in a single re-size. + * @param flash_incr_mode: Instance of the H5C_cache_flash_incr_mode enumerated + * type whose value indicates whether and by which algorithm we should + * make flash increases in the size of the cache to accommodate insertion + * of large entries and large increases in the size of a single entry. + * @param flash_multiple: Double containing the multiple described above in the + * H5C_flash_incr__add_space section of the discussion of the + * flash_incr_mode section. + * @param flash_threshold: Double containing the factor by which current max cache + * size is multiplied to obtain the size threshold for the add_space flash + * increment algorithm. + * @param decr_mode: Instance of the H5C_cache_decr_mode enumerated type whose + * value indicates how we determine whether the cache size should be + * decreased. + * @param upper_hr_threshold: Upper hit rate threshold. The use of this field + * varies according to the current decr_mode. + * @param decrement: This field is only used when the decr_mode is + * H5C_decr__threshold. + * @param apply_max_decrement: Boolean flag used to determine whether decrements + * in cache size are to be limited by the max_decrement field. + * @param max_decrement: Maximum number of bytes by which the cache size can be + * decreased in a single re-size. + * @param epochs_before_eviction: Integer field used in H5C_decr__age_out and + * H5C_decr__age_out_with_threshold decrement modes. + * @param apply_empty_reserve: Boolean field controlling whether the empty_reserve + * field is to be used in computing the new cache size when the + * decr_mode is H5C_decr__age_out or H5C_decr__age_out_with_threshold. + * @param empty_reserve: To avoid a constant racheting down of cache size by small + * amounts in the H5C_decr__age_out and H5C_decr__age_out_with_threshold + * modes. + * @param dirty_bytes_threshold: Threshold of dirty byte creation used to + * synchronize updates between caches. + * @param metadata_write_strategy: Integer field containing a code indicating the + * desired metadata write strategy. + */ public H5AC_cache_config_t (int version, boolean rpt_fcn_enabled, boolean open_trace_file, boolean close_trace_file, String trace_file_name, boolean evictions_enabled, boolean set_initial_size, long initial_size, double min_clean_fraction, long max_size, diff --git a/java/src/hdf/hdf5lib/structs/H5A_info_t.java b/java/src/hdf/hdf5lib/structs/H5A_info_t.java index a46a495..f2c10f0 100644 --- a/java/src/hdf/hdf5lib/structs/H5A_info_t.java +++ b/java/src/hdf/hdf5lib/structs/H5A_info_t.java @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -15,13 +14,20 @@ package hdf.hdf5lib.structs; import java.io.Serializable; -//Information struct for Attribute (For H5Aget_info/H5Aget_info_by_idx/H5Aget_info_by_name) +/** + * Information struct for Attribute (For H5Aget_info/H5Aget_info_by_idx/H5Aget_info_by_name) + * + */ public class H5A_info_t implements Serializable{ private static final long serialVersionUID = 2791443594041667613L; - public boolean corder_valid; // Indicate if creation order is valid - public long corder; // Creation order of attribute - public int cset; // Character set of attribute name - public long data_size; // Size of raw data + /** Indicate if creation order is valid */ + public boolean corder_valid; + /** Creation order of attribute */ + public long corder; + /** Character set of attribute name */ + public int cset; + /** Size of raw data */ + public long data_size; H5A_info_t(boolean corder_valid, long corder, int cset, long data_size) { this.corder_valid = corder_valid; diff --git a/java/src/hdf/hdf5lib/structs/H5E_error2_t.java b/java/src/hdf/hdf5lib/structs/H5E_error2_t.java index 257ad05..5981fc7 100644 --- a/java/src/hdf/hdf5lib/structs/H5E_error2_t.java +++ b/java/src/hdf/hdf5lib/structs/H5E_error2_t.java @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -15,17 +14,26 @@ package hdf.hdf5lib.structs; import java.io.Serializable; -//Information struct for Attribute (For H5Ewalk) +/** + * Information struct for Attribute (For H5Ewalk) + * + */ public class H5E_error2_t implements Serializable{ private static final long serialVersionUID = 279144359041667613L; - - public long cls_id; //class ID - public long maj_num; //major error ID - public long min_num; //minor error number - public int line; //line in file where error occurs - public String func_name; //function in which error occurred - public String file_name; //file in which error occurred - public String desc; //optional supplied description + /** class ID */ + public long cls_id; + /** major error ID */ + public long maj_num; + /** minor error number */ + public long min_num; + /** line in file where error occurs */ + public int line; + /** function in which error occurred */ + public String func_name; + /** file in which error occurred */ + public String file_name; + /** optional supplied description */ + public String desc; H5E_error2_t(long cls_id, long maj_num, long min_num, int line, String func_name, String file_name, String desc) { this.cls_id = cls_id; diff --git a/java/src/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java b/java/src/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java index 9fcff2e..5da4abd 100644 --- a/java/src/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java +++ b/java/src/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java @@ -16,7 +16,7 @@ package hdf.hdf5lib.structs; import java.io.Serializable; -/* +/** * Java representation of the HDFS VFD file access property list (fapl) * structure. * @@ -26,15 +26,31 @@ import java.io.Serializable; public class H5FD_hdfs_fapl_t implements Serializable { private static final long serialVersionUID = 2072473407027648309L; + /** Version number of the H5FD_hdfs_fapl_t structure. */ private int version; + /** Name of "Name Node" to access as the HDFS server. */ private String namenode_name; + /** Port number to use to connect with Name Node. */ private int namenode_port; + /** Username to use when accessing file. */ private String user_name; + /** Path to the location of the Kerberos authentication cache. */ private String kerberos_ticket_cache; + /** Size (in bytes) of the file read stream buffer. */ private int stream_buffer_size; - /* + /** * Create a fapl_t structure with the specified components. + * @param namenode_name + * Name of "Name Node" to access as the HDFS server. + * @param namenode_port + * Port number to use to connect with Name Node. + * @param user_name + * Username to use when accessing file. + * @param kerberos_ticket_cache + * Path to the location of the Kerberos authentication cache. + * @param stream_buffer_size + * Size (in bytes) of the file read stream buffer. */ public H5FD_hdfs_fapl_t( String namenode_name, diff --git a/java/src/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java b/java/src/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java index a899e10..39f5424 100644 --- a/java/src/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java +++ b/java/src/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java @@ -16,7 +16,7 @@ package hdf.hdf5lib.structs; import java.io.Serializable; -/* +/** * Java representation of the ROS3 VFD file access property list (fapl) * structure. * @@ -46,10 +46,15 @@ import java.io.Serializable; public class H5FD_ros3_fapl_t implements Serializable { private static final long serialVersionUID = 8985533001471224030L; + /** Version number of the H5FD_ros3_fapl_t structure */ private int version; + /** Flag TRUE or FALSE whether or not requests are to be authenticated with the AWS4 algorithm. */ private boolean authenticate; + /** region "aws region" for authenticating request */ private String aws_region; + /** id "secret id" or "access id" for authenticating request */ private String secret_id; + /** key "secret key" or "access key" for authenticating request */ private String secret_key; /** diff --git a/java/src/hdf/hdf5lib/structs/H5F_info2_t.java b/java/src/hdf/hdf5lib/structs/H5F_info2_t.java index 4664b5b..f951bb4 100644 --- a/java/src/hdf/hdf5lib/structs/H5F_info2_t.java +++ b/java/src/hdf/hdf5lib/structs/H5F_info2_t.java @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -15,19 +14,43 @@ package hdf.hdf5lib.structs; import java.io.Serializable; -//Information struct for object (for H5Fget_info) +/** + * Information struct for object (for H5Fget_info) + * + */ public class H5F_info2_t implements Serializable{ private static final long serialVersionUID = 4691681162544054518L; - public int super_version; // Superblock version # - public long super_size; // Superblock size - public long super_ext_size; // Superblock extension size - public int free_version; // Version # of file free space management - public long free_meta_size; // Free space manager metadata size - public long free_tot_space; // Amount of free space in the file - public int sohm_version; // Version # of shared object header info - public long sohm_hdr_size; // Shared object header message header size - public H5_ih_info_t sohm_msgs_info; // Shared object header message index & heap size + /** Superblock version number */ + public int super_version; + /** Superblock size */ + public long super_size; + /** Superblock extension size */ + public long super_ext_size; + /** Version number of file free space management */ + public int free_version; + /** Free space manager metadata size */ + public long free_meta_size; + /** Amount of free space in the file */ + public long free_tot_space; + /** Version number of shared object header info */ + public int sohm_version; + /** Shared object header message header size */ + public long sohm_hdr_size; + /** Shared object header message index and heap size */ + public H5_ih_info_t sohm_msgs_info; + /** + * Constructor fot current "global" information about file + * @param super_version: Superblock version number + * @param super_size: Superblock size + * @param super_ext_size: Superblock extension size + * @param free_version: Version number of file free space management + * @param free_meta_size: Free space manager metadata size + * @param free_tot_space: Amount of free space in the file + * @param sohm_version: Version number of shared object header info + * @param sohm_hdr_size: Shared object header message header size + * @param sohm_msgs_info: Shared object header message index and heap size + */ public H5F_info2_t (int super_version, long super_size, long super_ext_size, int free_version, long free_meta_size, long free_tot_space, int sohm_version, long sohm_hdr_size, H5_ih_info_t sohm_msgs_info) diff --git a/java/src/hdf/hdf5lib/structs/H5G_info_t.java b/java/src/hdf/hdf5lib/structs/H5G_info_t.java index 56c876e..e79f859 100644 --- a/java/src/hdf/hdf5lib/structs/H5G_info_t.java +++ b/java/src/hdf/hdf5lib/structs/H5G_info_t.java @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -15,11 +14,18 @@ package hdf.hdf5lib.structs; import java.io.Serializable; -//Information struct for group (for H5Gget_info/H5Gget_info_by_name/H5Gget_info_by_idx) +/** + * Information struct for group (for H5Gget_info/H5Gget_info_by_name/H5Gget_info_by_idx) + * + */ public class H5G_info_t implements Serializable{ private static final long serialVersionUID = -3746463015312132912L; - public int storage_type; // Type of storage for links in group - public long nlinks; // Number of links in group - public long max_corder; // Current max. creation order value for group - public boolean mounted; // Whether group has a file mounted on it + /** Type of storage for links in group */ + public int storage_type; + /** Number of links in group */ + public long nlinks; + /** Current max. creation order value for group */ + public long max_corder; + /** Whether group has a file mounted on it */ + public boolean mounted; } diff --git a/java/src/hdf/hdf5lib/structs/H5L_info_t.java b/java/src/hdf/hdf5lib/structs/H5L_info_t.java index 377e617..a3011c0 100644 --- a/java/src/hdf/hdf5lib/structs/H5L_info_t.java +++ b/java/src/hdf/hdf5lib/structs/H5L_info_t.java @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -17,17 +16,26 @@ import java.io.Serializable; import hdf.hdf5lib.HDF5Constants; -// Information struct for link (for H5Lget_info/H5Lget_info_by_idx) +/** + * Information struct for link (for H5Lget_info/H5Lget_info_by_idx) + * + */ public class H5L_info_t implements Serializable { private static final long serialVersionUID = -4754320605310155033L; + /** Type of link */ public int type; + /** Indicate if creation order is valid */ public boolean corder_valid; + /** Creation order */ public long corder; + /** Character set of link name */ public int cset; + /** Character set of link name */ public H5O_token_t token; + /** Size of a soft link or user-defined link value */ public long val_size; - // Constructor for using object token portion of C union + /** Constructor for using object token portion of C union */ H5L_info_t (int type, boolean corder_valid, long corder, int cset, H5O_token_t token) { @@ -39,7 +47,7 @@ public class H5L_info_t implements Serializable { this.val_size = -1; } - // Constructor for using val_size portion of C union + /** Constructor for using val_size portion of C union */ H5L_info_t (int type, boolean corder_valid, long corder, int cset, long val_size) { diff --git a/java/src/hdf/hdf5lib/structs/H5O_hdr_info_t.java b/java/src/hdf/hdf5lib/structs/H5O_hdr_info_t.java index 8d0cc24..2475dd9 100644 --- a/java/src/hdf/hdf5lib/structs/H5O_hdr_info_t.java +++ b/java/src/hdf/hdf5lib/structs/H5O_hdr_info_t.java @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -15,19 +14,32 @@ package hdf.hdf5lib.structs; import java.io.Serializable; -// Information struct for object header metadata (for H5Oget_info/H5Oget_info_by_name/H5Oget_info_by_idx) +/** + * Information struct for object header metadata (for H5Oget_info/H5Oget_info_by_name/H5Oget_info_by_idx) + * + */ public class H5O_hdr_info_t implements Serializable { private static final long serialVersionUID = 7883826382952577189L; - public int version; /* Version number of header format in file */ - public int nmesgs; /* Number of object header messages */ - public int nchunks; /* Number of object header chunks */ - public int flags; /* Object header status flags */ - public long space_total; /* Total space for storing object header in file */ - public long space_meta; /* Space within header for object header metadata information */ - public long space_mesg; /* Space within header for actual message information */ - public long space_free; /* Free space within object header */ - public long mesg_present; /* Flags to indicate presence of message type in header */ - public long mesg_shared; /* Flags to indicate message type is shared in header */ + /** Version number of header format in file */ + public int version; + /** Number of object header messages */ + public int nmesgs; + /** Number of object header chunks */ + public int nchunks; + /** Object header status flags */ + public int flags; + /** Total space for storing object header in file */ + public long space_total; + /** Space within header for object header metadata information */ + public long space_meta; + /** Space within header for actual message information */ + public long space_mesg; + /** Free space within object header */ + public long space_free; + /** Flags to indicate presence of message type in header */ + public long mesg_present; + /** Flags to indicate message type is shared in header */ + public long mesg_shared; H5O_hdr_info_t (int version, int nmesgs, int nchunks, int flags, long space_total, long space_meta, long space_mesg, long space_free, @@ -56,25 +68,25 @@ public class H5O_hdr_info_t implements Serializable { H5O_hdr_info_t info = (H5O_hdr_info_t) o; if (this.version != info.version) - return false; + return false; if (this.nmesgs != info.nmesgs) - return false; + return false; if (this.nchunks != info.nchunks) - return false; + return false; if (this.flags != info.flags) - return false; + return false; if (this.space_total != info.space_total) - return false; + return false; if (this.space_meta != info.space_meta) - return false; + return false; if (this.space_mesg != info.space_mesg) - return false; + return false; if (this.space_free != info.space_free) - return false; + return false; if (this.mesg_present != info.mesg_present) - return false; + return false; if (this.mesg_shared != info.mesg_shared) - return false; + return false; return true; } diff --git a/java/src/hdf/hdf5lib/structs/H5O_info_t.java b/java/src/hdf/hdf5lib/structs/H5O_info_t.java index 6a26a10..d2208d2 100644 --- a/java/src/hdf/hdf5lib/structs/H5O_info_t.java +++ b/java/src/hdf/hdf5lib/structs/H5O_info_t.java @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -15,19 +14,43 @@ package hdf.hdf5lib.structs; import java.io.Serializable; -// Information struct for object (for H5Oget_info/H5Oget_info_by_name/H5Oget_info_by_idx) +/** + * Information struct for object (for H5Oget_info/H5Oget_info_by_name/H5Oget_info_by_idx) + * + */ public class H5O_info_t implements Serializable { private static final long serialVersionUID = 4691681163544054518L; - public long fileno; /* File number that object is located in */ - public H5O_token_t token; /* Object token in file */ - public int type; /* Basic object type (group, dataset, etc.) */ - public int rc; /* Reference count of object */ - public long atime; /* Access time */ - public long mtime; /* Modification time */ - public long ctime; /* Change time */ - public long btime; /* Birth time */ - public long num_attrs; /* # of attributes attached to object */ + /** File number that object is located in */ + public long fileno; + /** Object token in file */ + public H5O_token_t token; + /** Basic object type (group, dataset, etc.) */ + public int type; + /** Reference count of object */ + public int rc; + /** Access time */ + public long atime; + /** Modification time */ + public long mtime; + /** Change time */ + public long ctime; + /** Birth time */ + public long btime; + /** Number of attributes attached to object */ + public long num_attrs; + /** Constructor for data model information struct for objects + * + * @param fileno: File number that object is located in + * @param token: Object token in file + * @param type: Basic object type + * @param rc: Reference count of object + * @param atime: Access time + * @param mtime: Modification time + * @param ctime: Change time + * @param btime: Birth time + * @param num_attrs: Number of attributes attached to object + */ public H5O_info_t (long fileno, H5O_token_t token, int type, int rc, long atime, long mtime, long ctime, long btime, long num_attrs) { diff --git a/java/src/hdf/hdf5lib/structs/H5O_native_info_t.java b/java/src/hdf/hdf5lib/structs/H5O_native_info_t.java index 4e80849..70e5231 100644 --- a/java/src/hdf/hdf5lib/structs/H5O_native_info_t.java +++ b/java/src/hdf/hdf5lib/structs/H5O_native_info_t.java @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -15,15 +14,20 @@ package hdf.hdf5lib.structs; import java.io.Serializable; -// Information struct for native HDF5 object info, such as object header metadata (for H5Oget_info/H5Oget_info_by_name/H5Oget_info_by_idx). +/** + * Information struct for native HDF5 object info, such as object header metadata (for H5Oget_info/H5Oget_info_by_name/H5Oget_info_by_idx). + * + */ public class H5O_native_info_t implements Serializable { private static final long serialVersionUID = 7883826382952577189L; - - public H5O_hdr_info_t hdr_info; /* Object header information */ + /** Object header information */ + public H5O_hdr_info_t hdr_info; /* Extra metadata storage for obj & attributes */ - public H5_ih_info_t obj_info; /* v1/v2 B-tree & local/fractal heap for groups, B-tree for chunked datasets */ - public H5_ih_info_t attr_info; /* v2 B-tree & heap for attributes */ + /** v1/v2 B-tree and local/fractal heap for groups, B-tree for chunked datasets */ + public H5_ih_info_t obj_info; + /** v2 B-tree and heap for attributes */ + public H5_ih_info_t attr_info; H5O_native_info_t (H5O_hdr_info_t oheader_info, H5_ih_info_t obj_info, H5_ih_info_t attr_info) { @@ -45,8 +49,8 @@ public class H5O_native_info_t implements Serializable { if (!this.hdr_info.equals(info.hdr_info) || !this.obj_info.equals(info.obj_info) || !this.attr_info.equals(info.attr_info)) - return false; + return false; return true; } -}
\ No newline at end of file +} diff --git a/java/src/hdf/hdf5lib/structs/H5O_token_t.java b/java/src/hdf/hdf5lib/structs/H5O_token_t.java index 8ec0b7f..f0bb978 100644 --- a/java/src/hdf/hdf5lib/structs/H5O_token_t.java +++ b/java/src/hdf/hdf5lib/structs/H5O_token_t.java @@ -5,7 +5,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -17,15 +17,28 @@ import java.util.Arrays; import hdf.hdf5lib.HDF5Constants; -// Object token, which is a unique and permanent identifier, for an HDF5 object within a container. +/** + * Object token, which is a unique and permanent identifier, for an HDF5 object within a container. + * + */ public class H5O_token_t implements Serializable { private static final long serialVersionUID = -4754320605310155032L; + /** + * Tokens are unique and permanent identifiers that are + * used to reference HDF5 objects in a container. + * Use basic byte array to store the dat + */ public byte[] data; H5O_token_t (byte[] data) { this.data = data; } + /** + * Check if token data is undefined + * + * @return true if token data is undefined + */ public boolean isUndefined() { return this.equals(HDF5Constants.H5O_TOKEN_UNDEF); } @@ -42,4 +55,4 @@ public class H5O_token_t implements Serializable { return Arrays.equals(this.data, token.data); } -}
\ No newline at end of file +} diff --git a/java/src/hdf/hdf5lib/structs/H5_ih_info_t.java b/java/src/hdf/hdf5lib/structs/H5_ih_info_t.java index 7159f02..0c6111b 100644 --- a/java/src/hdf/hdf5lib/structs/H5_ih_info_t.java +++ b/java/src/hdf/hdf5lib/structs/H5_ih_info_t.java @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -15,10 +14,15 @@ package hdf.hdf5lib.structs; import java.io.Serializable; -//Information struct for group (for H5Gget_info/H5Gget_info_by_name/H5Gget_info_by_idx) +/** + * Information struct for group (for H5Gget_info/H5Gget_info_by_name/H5Gget_info_by_idx) + * + */ public class H5_ih_info_t implements Serializable { private static final long serialVersionUID = -142238015615462707L; - public long index_size; /* btree and/or list */ + /** btree and/or list size of index */ + public long index_size; + /** btree and/or list size of hp */ public long heap_size; H5_ih_info_t (long index_size, long heap_size) @@ -38,9 +42,9 @@ public class H5_ih_info_t implements Serializable { H5_ih_info_t info = (H5_ih_info_t) o; if (this.index_size != info.index_size) - return false; + return false; if (this.heap_size != info.heap_size) - return false; + return false; return true; } diff --git a/java/src/jni/CMakeLists.txt b/java/src/jni/CMakeLists.txt index d945c33..ab306ef 100644 --- a/java/src/jni/CMakeLists.txt +++ b/java/src/jni/CMakeLists.txt @@ -45,6 +45,7 @@ set (HDF5_JAVA_JNI_CHDRS ${HDF5_JAVA_JNI_SOURCE_DIR}/h5fImp.h ${HDF5_JAVA_JNI_SOURCE_DIR}/h5gImp.h ${HDF5_JAVA_JNI_SOURCE_DIR}/h5iImp.h + ${HDF5_JAVA_JNI_SOURCE_DIR}/h5Imp.h ${HDF5_JAVA_JNI_SOURCE_DIR}/h5jni.h ${HDF5_JAVA_JNI_SOURCE_DIR}/h5lImp.h ${HDF5_JAVA_JNI_SOURCE_DIR}/h5oImp.h @@ -77,8 +78,9 @@ set (CMAKE_INCLUDE_CURRENT_DIR_IN_INTERFACE ON) ########### JNI libraries always must be built shared ############### add_library (${HDF5_JAVA_JNI_LIB_TARGET} SHARED ${HDF5_JAVA_JNI_CSRCS} ${HDF5_JAVA_JNI_CHDRS}) target_include_directories (${HDF5_JAVA_JNI_LIB_TARGET} - PRIVATE "${HDF5_SRC_DIR};${HDF5_BINARY_DIR};${HDF5_JAVA_JNI_SOURCE_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>" + PRIVATE "${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};${HDF5_JAVA_JNI_SOURCE_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>" ) +target_compile_options(${HDF5_JAVA_JNI_LIB_TARGET} PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (${HDF5_JAVA_JNI_LIB_TARGET} SHARED) target_link_libraries (${HDF5_JAVA_JNI_LIB_TARGET} PUBLIC ${HDF5_LIBSH_TARGET}) set_target_properties (${HDF5_JAVA_JNI_LIB_TARGET} PROPERTIES FOLDER libraries/jni) @@ -86,6 +88,13 @@ SET_GLOBAL_VARIABLE (HDF5_LIBRARIES_TO_EXPORT "${HDF5_LIBRARIES_TO_EXPORT};${HDF H5_SET_LIB_OPTIONS (${HDF5_JAVA_JNI_LIB_TARGET} ${HDF5_JAVA_JNI_LIB_NAME} SHARED "JAVA") #----------------------------------------------------------------------------- +# Add Target to clang-format +#----------------------------------------------------------------------------- +if (HDF5_ENABLE_FORMATTERS) + clang_format (HDF5_JNI_SRC_FORMAT ${HDF5_JAVA_JNI_LIB_TARGET}) +endif () + +#----------------------------------------------------------------------------- # Add Target(s) to CMake Install for import into other projects #----------------------------------------------------------------------------- if (HDF5_EXPORTED_TARGETS) diff --git a/java/src/jni/Makefile.am b/java/src/jni/Makefile.am index 1ec9b94..bf086d2 100644 --- a/java/src/jni/Makefile.am +++ b/java/src/jni/Makefile.am @@ -1,12 +1,11 @@ # # Copyright by The HDF Group. -# Copyright by the Board of Trustees of the University of Illinois. # All rights reserved. # # This file is part of HDF5. The full HDF5 copyright notice, including # terms governing use, modification, and redistribution, is contained in # the COPYING file, which can be found at the root of the source code -# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. +# distribution tree, or in https://www.hdfgroup.org/licenses. # If you do not have access to either file, you may request a copy from # help@hdfgroup.org. ## diff --git a/java/src/jni/Makefile.in b/java/src/jni/Makefile.in index 8ae3c7c..f9a8165 100644 --- a/java/src/jni/Makefile.in +++ b/java/src/jni/Makefile.in @@ -16,13 +16,12 @@ # # Copyright by The HDF Group. -# Copyright by the Board of Trustees of the University of Illinois. # All rights reserved. # # This file is part of HDF5. The full HDF5 copyright notice, including # terms governing use, modification, and redistribution, is contained in # the COPYING file, which can be found at the root of the source code -# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. +# distribution tree, or in https://www.hdfgroup.org/licenses. # If you do not have access to either file, you may request a copy from # help@hdfgroup.org. # @@ -114,6 +113,7 @@ am__aclocal_m4_deps = $(top_srcdir)/m4/aclocal_cxx.m4 \ $(top_srcdir)/m4/ax_check_junit.m4 \ $(top_srcdir)/m4/ax_java_options.m4 \ $(top_srcdir)/m4/ax_jni_include_dir.m4 \ + $(top_srcdir)/m4/ax_prog_doxygen.m4 \ $(top_srcdir)/m4/ax_prog_jar.m4 \ $(top_srcdir)/m4/ax_prog_java.m4 \ $(top_srcdir)/m4/ax_prog_java_works.m4 \ @@ -423,7 +423,7 @@ AMTAR = @AMTAR@ # H5_CFLAGS holds flags that should be used when building hdf5, # but which should not be exported to h5cc for building other programs. -# AM_CFLAGS is an automake construct which should be used by Makefiles +# AM_CFLAGS is an automake construct which should be used by Makefiles # instead of CFLAGS, as CFLAGS is reserved solely for the user to define. # This applies to FCFLAGS, CXXFLAGS, CPPFLAGS, and LDFLAGS as well. AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@ @@ -451,6 +451,7 @@ CC = @CC@ CCDEPMODE = @CCDEPMODE@ CC_VERSION = @CC_VERSION@ CFLAGS = @CFLAGS@ +CLANG_SANITIZE_CHECKS = @CLANG_SANITIZE_CHECKS@ CODESTACK = @CODESTACK@ CONFIG_DATE = @CONFIG_DATE@ CONFIG_MODE = @CONFIG_MODE@ @@ -467,11 +468,54 @@ DEFAULT_API_VERSION = @DEFAULT_API_VERSION@ DEFS = @DEFS@ DEPDIR = @DEPDIR@ DEPRECATED_SYMBOLS = @DEPRECATED_SYMBOLS@ -DEV_WARNINGS = @DEV_WARNINGS@ +DESIRED_FILE_LOCKING = @DESIRED_FILE_LOCKING@ +DIAGS = @DIAGS@ DIRECT_VFD = @DIRECT_VFD@ DLLTOOL = @DLLTOOL@ +DOXYGEN_EXAMPLES_DIRECTORY = @DOXYGEN_EXAMPLES_DIRECTORY@ +DOXYGEN_EXTERNAL_SEARCH = @DOXYGEN_EXTERNAL_SEARCH@ +DOXYGEN_HTML_EXTRA_FILES = @DOXYGEN_HTML_EXTRA_FILES@ +DOXYGEN_HTML_EXTRA_STYLESHEET = @DOXYGEN_HTML_EXTRA_STYLESHEET@ +DOXYGEN_HTML_FOOTER = @DOXYGEN_HTML_FOOTER@ +DOXYGEN_HTML_HEADER = @DOXYGEN_HTML_HEADER@ +DOXYGEN_INCLUDE_ALIASES = @DOXYGEN_INCLUDE_ALIASES@ +DOXYGEN_INPUT_DIRECTORY = @DOXYGEN_INPUT_DIRECTORY@ +DOXYGEN_LAYOUT_FILE = @DOXYGEN_LAYOUT_FILE@ +DOXYGEN_MACRO_EXPANSION = @DOXYGEN_MACRO_EXPANSION@ +DOXYGEN_OPTIMIZE_OUTPUT_FOR_C = @DOXYGEN_OPTIMIZE_OUTPUT_FOR_C@ +DOXYGEN_OUTPUT_DIRECTORY = @DOXYGEN_OUTPUT_DIRECTORY@ +DOXYGEN_PACKAGE = @DOXYGEN_PACKAGE@ +DOXYGEN_PAPER_SIZE = @DOXYGEN_PAPER_SIZE@ +DOXYGEN_PROJECT_BRIEF = @DOXYGEN_PROJECT_BRIEF@ +DOXYGEN_PROJECT_LOGO = @DOXYGEN_PROJECT_LOGO@ +DOXYGEN_SEARCHENGINE_URL = @DOXYGEN_SEARCHENGINE_URL@ +DOXYGEN_SERVER_BASED_SEARCH = @DOXYGEN_SERVER_BASED_SEARCH@ +DOXYGEN_VERSION_STRING = @DOXYGEN_VERSION_STRING@ DSYMUTIL = @DSYMUTIL@ DUMPBIN = @DUMPBIN@ +DX_CONFIG = @DX_CONFIG@ +DX_DOCDIR = @DX_DOCDIR@ +DX_DOT = @DX_DOT@ +DX_DOXYGEN = @DX_DOXYGEN@ +DX_DVIPS = @DX_DVIPS@ +DX_EGREP = @DX_EGREP@ +DX_ENV = @DX_ENV@ +DX_FLAG_chi = @DX_FLAG_chi@ +DX_FLAG_chm = @DX_FLAG_chm@ +DX_FLAG_doc = @DX_FLAG_doc@ +DX_FLAG_dot = @DX_FLAG_dot@ +DX_FLAG_html = @DX_FLAG_html@ +DX_FLAG_man = @DX_FLAG_man@ +DX_FLAG_pdf = @DX_FLAG_pdf@ +DX_FLAG_ps = @DX_FLAG_ps@ +DX_FLAG_rtf = @DX_FLAG_rtf@ +DX_FLAG_xml = @DX_FLAG_xml@ +DX_HHC = @DX_HHC@ +DX_LATEX = @DX_LATEX@ +DX_MAKEINDEX = @DX_MAKEINDEX@ +DX_PDFLATEX = @DX_PDFLATEX@ +DX_PERL = @DX_PERL@ +DX_PROJECT = @DX_PROJECT@ ECHO_C = @ECHO_C@ ECHO_N = @ECHO_N@ ECHO_T = @ECHO_T@ @@ -505,6 +549,7 @@ H5_CPPFLAGS = @H5_CPPFLAGS@ H5_CXXFLAGS = @H5_CXXFLAGS@ H5_FCFLAGS = @H5_FCFLAGS@ H5_FORTRAN_SHARED = @H5_FORTRAN_SHARED@ +H5_IS_DARWIN = @H5_IS_DARWIN@ H5_JAVACFLAGS = @H5_JAVACFLAGS@ H5_JAVAFLAGS = @H5_JAVAFLAGS@ H5_JNIFLAGS = @H5_JNIFLAGS@ @@ -515,6 +560,7 @@ HAVE_DMALLOC = @HAVE_DMALLOC@ HAVE_Fortran_INTEGER_SIZEOF_16 = @HAVE_Fortran_INTEGER_SIZEOF_16@ HAVE_LIBHDFS = @HAVE_LIBHDFS@ HAVE_PTHREAD = @HAVE_PTHREAD@ +HDF5_DOXYGEN = @HDF5_DOXYGEN@ HDF5_HL = @HDF5_HL@ HDF5_INTERFACES = @HDF5_INTERFACES@ HDF5_TESTS = @HDF5_TESTS@ @@ -527,6 +573,7 @@ HL = @HL@ HL_FOR = @HL_FOR@ HSIZE_T = @HSIZE_T@ HSSIZE_T = @HSSIZE_T@ +IGNORE_DISABLED_FILE_LOCKS = @IGNORE_DISABLED_FILE_LOCKS@ INSTALL = @INSTALL@ INSTALL_DATA = @INSTALL_DATA@ INSTALL_PROGRAM = @INSTALL_PROGRAM@ @@ -564,6 +611,7 @@ MAKEINFO = @MAKEINFO@ MANIFEST_TOOL = @MANIFEST_TOOL@ MAP_API = @MAP_API@ MEMORYALLOCSANITYCHECK = @MEMORYALLOCSANITYCHECK@ +MIRROR_VFD = @MIRROR_VFD@ MKDIR_P = @MKDIR_P@ MPE = @MPE@ NM = @NM@ @@ -600,6 +648,7 @@ PATH_SEPARATOR = @PATH_SEPARATOR@ PREADWRITE = @PREADWRITE@ PROFILING = @PROFILING@ RANLIB = @RANLIB@ +RECURSIVE_RW_LOCKS = @RECURSIVE_RW_LOCKS@ ROOT = @ROOT@ ROS3_VFD = @ROS3_VFD@ RUNPARALLEL = @RUNPARALLEL@ @@ -623,6 +672,7 @@ TIME = @TIME@ TR = @TR@ TRACE_API = @TRACE_API@ UNAME_INFO = @UNAME_INFO@ +USE_FILE_LOCKING = @USE_FILE_LOCKING@ USE_FILTER_DEFLATE = @USE_FILTER_DEFLATE@ USE_FILTER_SZIP = @USE_FILTER_SZIP@ USINGMEMCHECKER = @USINGMEMCHECKER@ @@ -715,15 +765,15 @@ LIBH5_HL = $(top_builddir)/hl/src/libhdf5_hl.la LIBH5F_HL = $(top_builddir)/hl/fortran/src/libhdf5hl_fortran.la LIBH5CPP_HL = $(top_builddir)/hl/c++/src/libhdf5_hl_cpp.la -# Note that in svn revision 19400 the '/' after DESTDIR in H5* variables below -# has been removed. According to the official description of DESTDIR by Gnu at -# http://www.gnu.org/prep/standards/html_node/DESTDIR.html, DESTDIR is -# prepended to the normal and complete install path that it precedes for the -# purpose of installing in a temporary directory which is useful for building -# rpms and other packages. The '/' after ${DESTDIR} will be followed by another -# '/' at the beginning of the normal install path. When DESTDIR is empty the -# path then begins with '//', which is incorrect and causes problems at least for -# Cygwin. +# Note that in svn revision 19400 the '/' after DESTDIR in H5* variables below +# has been removed. According to the official description of DESTDIR by Gnu at +# http://www.gnu.org/prep/standards/html_node/DESTDIR.html, DESTDIR is +# prepended to the normal and complete install path that it precedes for the +# purpose of installing in a temporary directory which is useful for building +# rpms and other packages. The '/' after ${DESTDIR} will be followed by another +# '/' at the beginning of the normal install path. When DESTDIR is empty the +# path then begins with '//', which is incorrect and causes problems at least for +# Cygwin. # Scripts used to build examples # If only shared libraries have been installed, have h5cc build examples with @@ -748,30 +798,30 @@ CHECK_CLEANFILES = *.chkexe *.chklog *.clog *.clog2 # See libtool versioning documentation online. # After making changes, run bin/reconfigure to update other configure related # files like Makefile.in. -LT_VERS_INTERFACE = 200 -LT_VERS_AGE = 0 +LT_VERS_INTERFACE = 201 +LT_VERS_AGE = 1 LT_VERS_REVISION = 0 -LT_CXX_VERS_INTERFACE = 200 +LT_CXX_VERS_INTERFACE = 201 LT_CXX_VERS_REVISION = 0 -LT_CXX_VERS_AGE = 0 -LT_F_VERS_INTERFACE = 200 +LT_CXX_VERS_AGE = 1 +LT_F_VERS_INTERFACE = 201 LT_F_VERS_REVISION = 0 -LT_F_VERS_AGE = 0 +LT_F_VERS_AGE = 1 LT_HL_VERS_INTERFACE = 200 -LT_HL_VERS_REVISION = 0 +LT_HL_VERS_REVISION = 1 LT_HL_VERS_AGE = 0 LT_HL_CXX_VERS_INTERFACE = 200 -LT_HL_CXX_VERS_REVISION = 0 +LT_HL_CXX_VERS_REVISION = 1 LT_HL_CXX_VERS_AGE = 0 LT_HL_F_VERS_INTERFACE = 200 -LT_HL_F_VERS_REVISION = 0 +LT_HL_F_VERS_REVISION = 1 LT_HL_F_VERS_AGE = 0 -LT_JAVA_VERS_INTERFACE = 200 +LT_JAVA_VERS_INTERFACE = 201 LT_JAVA_VERS_REVISION = 0 -LT_JAVA_VERS_AGE = 0 -LT_TOOLS_VERS_INTERFACE = 200 +LT_JAVA_VERS_AGE = 1 +LT_TOOLS_VERS_INTERFACE = 201 LT_TOOLS_VERS_REVISION = 0 -LT_TOOLS_VERS_AGE = 0 +LT_TOOLS_VERS_AGE = 1 # Mark this directory as part of the JNI API JAVA_API = yes @@ -805,7 +855,7 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES) \ PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS) \ $(EXTRA_PROG) -chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) +chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) TEST_EXTENSIONS = .sh SH_LOG_COMPILER = $(SHELL) AM_SH_LOG_FLAGS = @@ -1322,9 +1372,9 @@ uninstall-am: uninstall-libLTLIBRARIES # commands that should be executed even if a file with the same name already # exists. .PHONY: build-check-clean build-check-p build-check-s build-lib build-progs \ - build-tests check-clean check-install check-p check-s check-vfd \ - check-passthrough-vol install-doc lib progs tests uninstall-doc \ - _exec_check-s _test help + build-tests check-clean check-install check-p check-s check-vfd \ + check-passthrough-vol install-doc lib progs tests uninstall-doc \ + _exec_check-s _test help trace doxygen help: @$(top_srcdir)/bin/makehelp diff --git a/java/src/jni/exceptionImp.c b/java/src/jni/exceptionImp.c index c5e7d85..12ef0a1 100644 --- a/java/src/jni/exceptionImp.c +++ b/java/src/jni/exceptionImp.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -262,12 +262,25 @@ done: * exception. */ jboolean -h5outOfMemory(JNIEnv *env, const char *functName) +h5outOfMemory(JNIEnv *env, const char *message) { - return H5JNIErrorClass(env, functName, "java/lang/OutOfMemoryError"); + return H5JNIErrorClass(env, message, "java/lang/OutOfMemoryError"); } /* end h5outOfMemory() */ /* + * Create and throw an 'AssertionError' + * + * Note: This routine never returns from the 'throw', + * and the Java native method immediately raises the + * exception. + */ +jboolean +h5assertion(JNIEnv *env, const char *message) +{ + return H5JNIErrorClass(env, message, "java/lang/AssertionError"); +} /* end h5assertion() */ + +/* * A fatal error in a JNI call * Create and throw an 'InternalError' * @@ -276,9 +289,9 @@ h5outOfMemory(JNIEnv *env, const char *functName) * exception. */ jboolean -h5JNIFatalError(JNIEnv *env, const char *functName) +h5JNIFatalError(JNIEnv *env, const char *message) { - return H5JNIErrorClass(env, functName, "java/lang/InternalError"); + return H5JNIErrorClass(env, message, "java/lang/InternalError"); } /* end h5JNIFatalError() */ /* @@ -290,9 +303,9 @@ h5JNIFatalError(JNIEnv *env, const char *functName) * exception. */ jboolean -h5nullArgument(JNIEnv *env, const char *functName) +h5nullArgument(JNIEnv *env, const char *message) { - return H5JNIErrorClass(env, functName, "java/lang/NullPointerException"); + return H5JNIErrorClass(env, message, "java/lang/NullPointerException"); } /* end h5nullArgument() */ /* @@ -304,9 +317,9 @@ h5nullArgument(JNIEnv *env, const char *functName) * exception. */ jboolean -h5badArgument(JNIEnv *env, const char *functName) +h5badArgument(JNIEnv *env, const char *message) { - return H5JNIErrorClass(env, functName, "java/lang/IllegalArgumentException"); + return H5JNIErrorClass(env, message, "java/lang/IllegalArgumentException"); } /* end h5badArgument() */ /* @@ -318,9 +331,9 @@ h5badArgument(JNIEnv *env, const char *functName) * exception. */ jboolean -h5unimplemented(JNIEnv *env, const char *functName) +h5unimplemented(JNIEnv *env, const char *message) { - return H5JNIErrorClass(env, functName, "java/lang/UnsupportedOperationException"); + return H5JNIErrorClass(env, message, "java/lang/UnsupportedOperationException"); } /* end h5unimplemented() */ /* h5raiseException(). This routine is called to generate diff --git a/java/src/jni/exceptionImp.h b/java/src/jni/exceptionImp.h index 1a7ad92..38469df 100644 --- a/java/src/jni/exceptionImp.h +++ b/java/src/jni/exceptionImp.h @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -14,8 +13,8 @@ #include <jni.h> /* Header for class hdf_hdf5lib_H5_exception */ -#ifndef _Included_hdf_hdf5lib_H5_exception -#define _Included_hdf_hdf5lib_H5_exception +#ifndef Included_hdf_hdf5lib_H5_exception +#define Included_hdf_hdf5lib_H5_exception #ifdef __cplusplus extern "C" { @@ -68,4 +67,4 @@ JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_exceptions_HDF5LibraryException__1getMi } /* end extern "C" */ #endif /* __cplusplus */ -#endif /* _Included_hdf_hdf5lib_H5_exception */ +#endif /* Included_hdf_hdf5lib_H5_exception */ diff --git a/java/src/jni/h5Constants.c b/java/src/jni/h5Constants.c index b884d2d..ee1448b 100644 --- a/java/src/jni/h5Constants.c +++ b/java/src/jni/h5Constants.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -26,8 +26,8 @@ extern "C" { #include <stdlib.h> #include "h5jni.h" -H5_GCC_DIAG_OFF(missing - prototypes) -H5_GCC_DIAG_OFF(unused - parameter) +H5_GCC_DIAG_OFF("missing-prototypes") +H5_GCC_DIAG_OFF("unused-parameter") JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5_1QUARTER_1HADDR_1MAX(JNIEnv *env, jclass cls) @@ -355,6 +355,11 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1BADGROUP(JNIEnv *env, jclass cls) return H5E_BADGROUP; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1BADITER(JNIEnv *env, jclass cls) +{ + return H5E_BADITER; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1BADMESG(JNIEnv *env, jclass cls) { return H5E_BADMESG; @@ -404,8 +409,26 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANAPPLY(JNIEnv *env, jclass cls) { return H5E_CANAPPLY; } -/*JNIEXPORT jlong JNICALL -Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTALLOC(JNIEnv *env, jclass cls) { return H5E_CANTALLOC; }*/ +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTALLOC(JNIEnv *env, jclass cls) +{ + return H5E_CANTALLOC; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTAPPEND(JNIEnv *env, jclass cls) +{ + return H5E_CANTAPPEND; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTATTACH(JNIEnv *env, jclass cls) +{ + return H5E_CANTATTACH; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCLEAN(JNIEnv *env, jclass cls) +{ + return H5E_CANTCLEAN; +} JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCLIP(JNIEnv *env, jclass cls) { @@ -417,6 +440,21 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCLOSEFILE(JNIEnv *env, jclass cls) return H5E_CANTCLOSEFILE; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCLOSEOBJ(JNIEnv *env, jclass cls) +{ + return H5E_CANTCLOSEOBJ; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCOMPARE(JNIEnv *env, jclass cls) +{ + return H5E_CANTCOMPARE; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCOMPUTE(JNIEnv *env, jclass cls) +{ + return H5E_CANTCOMPUTE; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCONVERT(JNIEnv *env, jclass cls) { return H5E_CANTCONVERT; @@ -427,6 +465,11 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCOPY(JNIEnv *env, jclass cls) return H5E_CANTCOPY; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCORK(JNIEnv *env, jclass cls) +{ + return H5E_CANTCORK; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTCOUNT(JNIEnv *env, jclass cls) { return H5E_CANTCOUNT; @@ -457,11 +500,36 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTDELETEFILE(JNIEnv *env, jclass cls) return H5E_CANTDELETEFILE; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTDEPEND(JNIEnv *env, jclass cls) +{ + return H5E_CANTDEPEND; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTDIRTY(JNIEnv *env, jclass cls) +{ + return H5E_CANTDIRTY; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTFILTER(JNIEnv *env, jclass cls) +{ + return H5E_CANTFILTER; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTENCODE(JNIEnv *env, jclass cls) { return H5E_CANTENCODE; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTEXPUNGE(JNIEnv *env, jclass cls) +{ + return H5E_CANTEXPUNGE; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTEXTEND(JNIEnv *env, jclass cls) +{ + return H5E_CANTEXTEND; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTFLUSH(JNIEnv *env, jclass cls) { return H5E_CANTFLUSH; @@ -472,11 +540,26 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTFREE(JNIEnv *env, jclass cls) return H5E_CANTFREE; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTGATHER(JNIEnv *env, jclass cls) +{ + return H5E_CANTGATHER; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTGC(JNIEnv *env, jclass cls) +{ + return H5E_CANTGC; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTGET(JNIEnv *env, jclass cls) { return H5E_CANTGET; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTGETSIZE(JNIEnv *env, jclass cls) +{ + return H5E_CANTGETSIZE; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTINC(JNIEnv *env, jclass cls) { return H5E_CANTINC; @@ -487,6 +570,11 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTINIT(JNIEnv *env, jclass cls) return H5E_CANTINIT; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTINS(JNIEnv *env, jclass cls) +{ + return H5E_CANTINS; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTINSERT(JNIEnv *env, jclass cls) { return H5E_CANTINSERT; @@ -507,11 +595,56 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTLOCK(JNIEnv *env, jclass cls) return H5E_CANTLOCK; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTLOCKFILE(JNIEnv *env, jclass cls) +{ + return H5E_CANTLOCKFILE; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTMARKCLEAN(JNIEnv *env, jclass cls) +{ + return H5E_CANTMARKCLEAN; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTMARKDIRTY(JNIEnv *env, jclass cls) +{ + return H5E_CANTMARKDIRTY; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTMARKSERIALIZED(JNIEnv *env, jclass cls) +{ + return H5E_CANTMARKSERIALIZED; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTMARKUNSERIALIZED(JNIEnv *env, jclass cls) +{ + return H5E_CANTMARKUNSERIALIZED; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTMERGE(JNIEnv *env, jclass cls) +{ + return H5E_CANTMERGE; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTMODIFY(JNIEnv *env, jclass cls) +{ + return H5E_CANTMODIFY; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTMOVE(JNIEnv *env, jclass cls) +{ + return H5E_CANTMOVE; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTNEXT(JNIEnv *env, jclass cls) { return H5E_CANTNEXT; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTNOTIFY(JNIEnv *env, jclass cls) +{ + return H5E_CANTNOTIFY; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTOPENFILE(JNIEnv *env, jclass cls) { return H5E_CANTOPENFILE; @@ -521,8 +654,36 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTOPENOBJ(JNIEnv *env, jclass cls) { return H5E_CANTOPENOBJ; } -/*JNIEXPORT jlong JNICALL -Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTRECV(JNIEnv *env, jclass cls) { return H5E_CANTRECV; }*/ +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTOPERATE(JNIEnv *env, jclass cls) +{ + return H5E_CANTOPERATE; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTPACK(JNIEnv *env, jclass cls) +{ + return H5E_CANTPACK; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTPIN(JNIEnv *env, jclass cls) +{ + return H5E_CANTPIN; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTPROTECT(JNIEnv *env, jclass cls) +{ + return H5E_CANTPROTECT; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTRECV(JNIEnv *env, jclass cls) +{ + return H5E_CANTRECV; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTREDISTRIBUTE(JNIEnv *env, jclass cls) +{ + return H5E_CANTREDISTRIBUTE; +} JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTREGISTER(JNIEnv *env, jclass cls) { @@ -534,6 +695,41 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTRELEASE(JNIEnv *env, jclass cls) return H5E_CANTRELEASE; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTREMOVE(JNIEnv *env, jclass cls) +{ + return H5E_CANTREMOVE; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTRENAME(JNIEnv *env, jclass cls) +{ + return H5E_CANTRENAME; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTRESET(JNIEnv *env, jclass cls) +{ + return H5E_CANTRESET; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTRESIZE(JNIEnv *env, jclass cls) +{ + return H5E_CANTRESIZE; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTRESTORE(JNIEnv *env, jclass cls) +{ + return H5E_CANTRESTORE; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTREVIVE(JNIEnv *env, jclass cls) +{ + return H5E_CANTREVIVE; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTSHRINK(JNIEnv *env, jclass cls) +{ + return H5E_CANTSHRINK; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTSELECT(JNIEnv *env, jclass cls) { return H5E_CANTSELECT; @@ -544,16 +740,71 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTSET(JNIEnv *env, jclass cls) return H5E_CANTSET; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTSERIALIZE(JNIEnv *env, jclass cls) +{ + return H5E_CANTSERIALIZE; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTSORT(JNIEnv *env, jclass cls) +{ + return H5E_CANTSORT; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTSPLIT(JNIEnv *env, jclass cls) { return H5E_CANTSPLIT; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTSWAP(JNIEnv *env, jclass cls) +{ + return H5E_CANTSWAP; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTTAG(JNIEnv *env, jclass cls) +{ + return H5E_CANTTAG; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUNCORK(JNIEnv *env, jclass cls) +{ + return H5E_CANTUNCORK; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUNDEPEND(JNIEnv *env, jclass cls) +{ + return H5E_CANTUNDEPEND; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUNLOCK(JNIEnv *env, jclass cls) { return H5E_CANTUNLOCK; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUNLOCKFILE(JNIEnv *env, jclass cls) +{ + return H5E_CANTUNLOCKFILE; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUNPIN(JNIEnv *env, jclass cls) +{ + return H5E_CANTUNPIN; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUNPROTECT(JNIEnv *env, jclass cls) +{ + return H5E_CANTUNPROTECT; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUNSERIALIZE(JNIEnv *env, jclass cls) +{ + return H5E_CANTUNSERIALIZE; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUPDATE(JNIEnv *env, jclass cls) +{ + return H5E_CANTUPDATE; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1CLOSEERROR(JNIEnv *env, jclass cls) { return H5E_CLOSEERROR; @@ -564,6 +815,11 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1COMPLEN(JNIEnv *env, jclass cls) return H5E_COMPLEN; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1CONTEXT(JNIEnv *env, jclass cls) +{ + return H5E_CONTEXT; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1DATASET(JNIEnv *env, jclass cls) { return H5E_DATASET; @@ -589,16 +845,31 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1DUPCLASS(JNIEnv *env, jclass cls) return H5E_DUPCLASS; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1EARRAY(JNIEnv *env, jclass cls) +{ + return H5E_EARRAY; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1EFL(JNIEnv *env, jclass cls) { return H5E_EFL; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1ERROR(JNIEnv *env, jclass cls) +{ + return H5E_ERROR; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1EXISTS(JNIEnv *env, jclass cls) { return H5E_EXISTS; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1FARRAY(JNIEnv *env, jclass cls) +{ + return H5E_FARRAY; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1FCNTL(JNIEnv *env, jclass cls) { return H5E_FCNTL; @@ -619,6 +890,11 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1FILEOPEN(JNIEnv *env, jclass cls) return H5E_FILEOPEN; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1FSPACE(JNIEnv *env, jclass cls) +{ + return H5E_FSPACE; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1FUNC(JNIEnv *env, jclass cls) { return H5E_FUNC; @@ -629,6 +905,11 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1HEAP(JNIEnv *env, jclass cls) return H5E_HEAP; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1INCONSISTENTSTATE(JNIEnv *env, jclass cls) +{ + return H5E_INCONSISTENTSTATE; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1INTERNAL(JNIEnv *env, jclass cls) { return H5E_INTERNAL; @@ -648,11 +929,21 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1LINKCOUNT(JNIEnv *env, jclass cls) { return H5E_LINKCOUNT; } +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1LOGGING(JNIEnv *env, jclass cls) +{ + return H5E_LOGGING; +} JNIEXPORT jint JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1MAJOR(JNIEnv *env, jclass cls) { return H5E_MAJOR; } +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1MAP(JNIEnv *env, jclass cls) +{ + return H5E_MAP; +} JNIEXPORT jint JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1MINOR(JNIEnv *env, jclass cls) { @@ -674,6 +965,21 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1MPIERRSTR(JNIEnv *env, jclass cls) return H5E_MPIERRSTR; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1NLINKS(JNIEnv *env, jclass cls) +{ + return H5E_NLINKS; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1NO_1INDEPENDENT(JNIEnv *env, jclass cls) +{ + return H5E_NO_INDEPENDENT; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1NOENCODER(JNIEnv *env, jclass cls) +{ + return H5E_NOENCODER; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1NOFILTER(JNIEnv *env, jclass cls) { return H5E_NOFILTER; @@ -714,16 +1020,41 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1NOTHDF5(JNIEnv *env, jclass cls) return H5E_NOTHDF5; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1NOTREGISTERED(JNIEnv *env, jclass cls) +{ + return H5E_NOTREGISTERED; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1OBJOPEN(JNIEnv *env, jclass cls) +{ + return H5E_OBJOPEN; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1OHDR(JNIEnv *env, jclass cls) { return H5E_OHDR; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1OPENERROR(JNIEnv *env, jclass cls) +{ + return H5E_OPENERROR; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1OVERFLOW(JNIEnv *env, jclass cls) { return H5E_OVERFLOW; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1PAGEBUF(JNIEnv *env, jclass cls) +{ + return H5E_PAGEBUF; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1PATH(JNIEnv *env, jclass cls) +{ + return H5E_PATH; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1PLINE(JNIEnv *env, jclass cls) { return H5E_PLINE; @@ -734,6 +1065,11 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1PLIST(JNIEnv *env, jclass cls) return H5E_PLIST; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1PLUGIN(JNIEnv *env, jclass cls) +{ + return H5E_PLUGIN; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1PROTECT(JNIEnv *env, jclass cls) { return H5E_PROTECT; @@ -764,11 +1100,26 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1SEEKERROR(JNIEnv *env, jclass cls) return H5E_SEEKERROR; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1SETDISALLOWED(JNIEnv *env, jclass cls) +{ + return H5E_SETDISALLOWED; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1SETLOCAL(JNIEnv *env, jclass cls) { return H5E_SETLOCAL; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1SLIST(JNIEnv *env, jclass cls) +{ + return H5E_SLIST; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1SOHM(JNIEnv *env, jclass cls) +{ + return H5E_SOHM; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1STORAGE(JNIEnv *env, jclass cls) { return H5E_STORAGE; @@ -779,6 +1130,21 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1SYM(JNIEnv *env, jclass cls) return H5E_SYM; } JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1SYSERRSTR(JNIEnv *env, jclass cls) +{ + return H5E_SYSERRSTR; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1SYSTEM(JNIEnv *env, jclass cls) +{ + return H5E_SYSTEM; +} +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_HDF5Constants_H5E_1TRAVERSE(JNIEnv *env, jclass cls) +{ + return H5E_TRAVERSE; +} +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_HDF5Constants_H5E_1TRUNCATED(JNIEnv *env, jclass cls) { return H5E_TRUNCATED; @@ -851,7 +1217,7 @@ Java_hdf_hdf5lib_HDF5Constants_H5ES_1STATUS_1CANCELED(JNIEnv *env, jclass cls) } /* Java does not have unsigned native types */ -H5_GCC_DIAG_OFF(sign - conversion) +H5_GCC_DIAG_OFF("sign-conversion") JNIEXPORT jint JNICALL Java_hdf_hdf5lib_HDF5Constants_H5F_1ACC_1CREAT(JNIEnv *env, jclass cls) { @@ -892,7 +1258,7 @@ Java_hdf_hdf5lib_HDF5Constants_H5F_1ACC_1SWMR_1WRITE(JNIEnv *env, jclass cls) { return H5F_ACC_SWMR_WRITE; } -H5_GCC_DIAG_ON(sign - conversion) +H5_GCC_DIAG_ON("sign-conversion") JNIEXPORT jint JNICALL Java_hdf_hdf5lib_HDF5Constants_H5F_1CLOSE_1DEFAULT(JNIEnv *env, jclass cls) @@ -1037,7 +1403,7 @@ Java_hdf_hdf5lib_HDF5Constants_H5FD_1DIRECT(JNIEnv *env, jclass cls) #ifdef H5_HAVE_DIRECT return H5FD_DIRECT; #else - return -1; + return H5I_INVALID_HID; #endif } JNIEXPORT jlong JNICALL @@ -1051,7 +1417,7 @@ Java_hdf_hdf5lib_HDF5Constants_H5FD_1HDFS(JNIEnv *env, jclass cls) #ifdef H5_HAVE_LIBHDFS return H5FD_HDFS; #else - return -1; + return H5I_INVALID_HID; #endif } JNIEXPORT jlong JNICALL @@ -1080,7 +1446,7 @@ Java_hdf_hdf5lib_HDF5Constants_H5FD_1ROS3(JNIEnv *env, jclass cls) #ifdef H5_HAVE_ROS3_VFD return H5FD_ROS3; #else - return -1; + return H5I_INVALID_HID; #endif } JNIEXPORT jlong JNICALL @@ -1094,7 +1460,7 @@ Java_hdf_hdf5lib_HDF5Constants_H5FD_1WINDOWS(JNIEnv *env, jclass cls) #ifdef H5_HAVE_WINDOWS return H5FD_DIRECT; #else - return -1; + return H5I_INVALID_HID; #endif } JNIEXPORT jint JNICALL @@ -3358,8 +3724,8 @@ Java_hdf_hdf5lib_HDF5Constants_H5Z_1FILTER_1ALL(JNIEnv *env, jclass cls) return H5Z_FILTER_ALL; } -H5_GCC_DIAG_ON(missing - prototypes) -H5_GCC_DIAG_ON(unused - parameter) +H5_GCC_DIAG_ON("missing-prototypes") +H5_GCC_DIAG_ON("unused-parameter") #ifdef __cplusplus } /* end extern "C" */ diff --git a/java/src/jni/h5Imp.c b/java/src/jni/h5Imp.c index 5773fff..691c98c 100644 --- a/java/src/jni/h5Imp.c +++ b/java/src/jni/h5Imp.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/jni/h5Imp.h b/java/src/jni/h5Imp.h index 696d7d2..8ab7662 100644 --- a/java/src/jni/h5Imp.h +++ b/java/src/jni/h5Imp.h @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -14,8 +13,8 @@ #include <jni.h> /* Header for class hdf_hdf5lib_H5_H5 */ -#ifndef _Included_hdf_hdf5lib_H5_H5 -#define _Included_hdf_hdf5lib_H5_H5 +#ifndef Included_hdf_hdf5lib_H5_H5 +#define Included_hdf_hdf5lib_H5_H5 #ifdef __cplusplus extern "C" { @@ -83,4 +82,4 @@ JNIEXPORT jboolean JNICALL Java_hdf_hdf5lib_H5_H5is_1library_1threadsafe(JNIEnv } /* end extern "C" */ #endif /* __cplusplus */ -#endif /* _Included_hdf_hdf5lib_H5_H5 */ +#endif /* Included_hdf_hdf5lib_H5_H5 */ diff --git a/java/src/jni/h5aImp.c b/java/src/jni/h5aImp.c index fe3dfef..6bf86d0 100644 --- a/java/src/jni/h5aImp.c +++ b/java/src/jni/h5aImp.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -1133,7 +1133,7 @@ H5AreadVL_asstr(JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf) for (i = 0; i < (size_t)n; i++) { h5str.s[0] = '\0'; - if (!h5str_sprintf(ENVONLY, &h5str, aid, tid, &(((char *)readBuf)[i * typeSize]), typeSize, 0)) + if (!h5str_sprintf(ENVONLY, &h5str, aid, tid, &(((char *)readBuf)[i * typeSize]), 0)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); if (NULL == (jstr = ENVPTR->NewStringUTF(ENVONLY, h5str.s))) @@ -1425,7 +1425,7 @@ Java_hdf_hdf5lib_H5_H5Aread_1reg_1ref(JNIEnv *env, jclass clss, jlong attr_id, j for (i = 0; i < n; i++) { h5str.s[0] = '\0'; - if (!h5str_sprintf(ENVONLY, &h5str, (hid_t)attr_id, (hid_t)mem_type_id, (void *)&ref_data[i], 0, 0)) + if (!h5str_sprintf(ENVONLY, &h5str, (hid_t)attr_id, (hid_t)mem_type_id, (void *)&ref_data[i], 0)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); if (NULL == (jstr = ENVPTR->NewStringUTF(ENVONLY, h5str.s))) @@ -2166,7 +2166,7 @@ H5A_iterate_cb(hid_t g_id, const char *name, const H5A_info_t *info, void *cb_da jobject visit_callback = wrapper->visit_callback; jstring str; JNIEnv * cbenv = NULL; - jclass cls; + jclass cbcls; jvalue args[4]; void * op_data = (void *)wrapper->op_data; jint status = -1; @@ -2176,12 +2176,12 @@ H5A_iterate_cb(hid_t g_id, const char *name, const H5A_info_t *info, void *cb_da H5_JNI_FATAL_ERROR(CBENVONLY, "H5A_iterate_cb: failed to attach current thread to JVM"); } - if (NULL == (cls = CBENVPTR->GetObjectClass(CBENVONLY, visit_callback))) + if (NULL == (cbcls = CBENVPTR->GetObjectClass(CBENVONLY, visit_callback))) CHECK_JNI_EXCEPTION(CBENVONLY, JNI_FALSE); if (NULL == (mid = CBENVPTR->GetMethodID( - CBENVONLY, cls, "callback", + CBENVONLY, cbcls, "callback", "(JLjava/lang/String;Lhdf/hdf5lib/structs/H5A_info_t;Lhdf/hdf5lib/callbacks/H5A_iterate_t;)I"))) CHECK_JNI_EXCEPTION(CBENVONLY, JNI_FALSE); diff --git a/java/src/jni/h5aImp.h b/java/src/jni/h5aImp.h index d3a4246..aee0e40 100644 --- a/java/src/jni/h5aImp.h +++ b/java/src/jni/h5aImp.h @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -14,8 +13,8 @@ #include <jni.h> /* Header for class hdf_hdf5lib_H5_H5A */ -#ifndef _Included_hdf_hdf5lib_H5_H5A -#define _Included_hdf_hdf5lib_H5_H5A +#ifndef Included_hdf_hdf5lib_H5_H5A +#define Included_hdf_hdf5lib_H5_H5A #ifdef __cplusplus extern "C" { @@ -376,4 +375,4 @@ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Aiterate_1by_1name(JNIEnv *, jclass } /* end extern "C" */ #endif /* __cplusplus */ -#endif /* _Included_hdf_hdf5lib_H5_H5A */ +#endif /* Included_hdf_hdf5lib_H5_H5A */ diff --git a/java/src/jni/h5dImp.c b/java/src/jni/h5dImp.c index b34fe25..73b252a 100644 --- a/java/src/jni/h5dImp.c +++ b/java/src/jni/h5dImp.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -1290,7 +1290,7 @@ H5DreadVL_asstr(JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid for (i = 0; i < (size_t)n; i++) { h5str.s[0] = '\0'; - if (!h5str_sprintf(ENVONLY, &h5str, did, tid, &(((char *)readBuf)[i * typeSize]), typeSize, 0)) + if (!h5str_sprintf(ENVONLY, &h5str, did, tid, &(((char *)readBuf)[i * typeSize]), 0)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); if (NULL == (jstr = ENVPTR->NewStringUTF(ENVONLY, h5str.s))) @@ -1669,8 +1669,7 @@ Java_hdf_hdf5lib_H5_H5Dread_1reg_1ref(JNIEnv *env, jclass clss, jlong dataset_id for (i = 0; i < n; i++) { h5str.s[0] = '\0'; - if (!h5str_sprintf(ENVONLY, &h5str, (hid_t)dataset_id, (hid_t)mem_type_id, (void *)&ref_data[i], 0, - 0)) + if (!h5str_sprintf(ENVONLY, &h5str, (hid_t)dataset_id, (hid_t)mem_type_id, (void *)&ref_data[i], 0)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); if (NULL == (jstr = ENVPTR->NewStringUTF(ENVONLY, h5str.s))) diff --git a/java/src/jni/h5dImp.h b/java/src/jni/h5dImp.h index b9ad1bb..e339dad 100644 --- a/java/src/jni/h5dImp.h +++ b/java/src/jni/h5dImp.h @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -14,8 +13,8 @@ #include <jni.h> /* Header for class hdf_hdf5lib_H5_H5D */ -#ifndef _Included_hdf_hdf5lib_H5_H5D -#define _Included_hdf_hdf5lib_H5_H5D +#ifndef Included_hdf_hdf5lib_H5_H5D +#define Included_hdf_hdf5lib_H5_H5D #ifdef __cplusplus extern "C" { @@ -323,4 +322,4 @@ JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Drefresh(JNIEnv *, jclass, jlong); } /* end extern "C" */ #endif /* __cplusplus */ -#endif /* _Included_hdf_hdf5lib_H5_H5D */ +#endif /* Included_hdf_hdf5lib_H5_H5D */ diff --git a/java/src/jni/h5eImp.c b/java/src/jni/h5eImp.c index 56c596d..5bdeae8 100644 --- a/java/src/jni/h5eImp.c +++ b/java/src/jni/h5eImp.c @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -508,7 +507,7 @@ H5E_walk_cb(int nindx, const H5E_error2_t *info, void *cb_data) jobject cb_info_t = NULL; jvalue args[7]; JNIEnv * cbenv = NULL; - jclass cls; + jclass cbcls; void * op_data = (void *)wrapper->op_data; jint status = FAIL; @@ -517,11 +516,11 @@ H5E_walk_cb(int nindx, const H5E_error2_t *info, void *cb_data) H5_JNI_FATAL_ERROR(CBENVONLY, "H5E_walk_cb: failed to attach current thread to JVM"); } - if (NULL == (cls = CBENVPTR->GetObjectClass(CBENVONLY, visit_callback))) + if (NULL == (cbcls = CBENVPTR->GetObjectClass(CBENVONLY, visit_callback))) CHECK_JNI_EXCEPTION(CBENVONLY, JNI_FALSE); if (NULL == (mid = CBENVPTR->GetMethodID( - CBENVONLY, cls, "callback", + CBENVONLY, cbcls, "callback", "(ILhdf/hdf5lib/structs/H5E_error2_t;Lhdf/hdf5lib/callbacks/H5E_walk_t;)I"))) CHECK_JNI_EXCEPTION(CBENVONLY, JNI_FALSE); diff --git a/java/src/jni/h5eImp.h b/java/src/jni/h5eImp.h index 4754965..95e43fa 100644 --- a/java/src/jni/h5eImp.h +++ b/java/src/jni/h5eImp.h @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -14,8 +13,8 @@ #include <jni.h> /* Header for class hdf_hdf5lib_H5_H5E */ -#ifndef _Included_hdf_hdf5lib_H5_H5E -#define _Included_hdf_hdf5lib_H5_H5E +#ifndef Included_hdf_hdf5lib_H5_H5E +#define Included_hdf_hdf5lib_H5_H5E #ifdef __cplusplus extern "C" { @@ -145,4 +144,4 @@ JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Ewalk2(JNIEnv *, jclass, jlong, jlo } /* end extern "C" */ #endif /* __cplusplus */ -#endif /* _Included_hdf_hdf5lib_H5_H5E */ +#endif /* Included_hdf_hdf5lib_H5_H5E */ diff --git a/java/src/jni/h5fImp.c b/java/src/jni/h5fImp.c index 76c5ad7..e59a69e 100644 --- a/java/src/jni/h5fImp.c +++ b/java/src/jni/h5fImp.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/jni/h5fImp.h b/java/src/jni/h5fImp.h index 6696218..bf2f199 100644 --- a/java/src/jni/h5fImp.h +++ b/java/src/jni/h5fImp.h @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -14,8 +13,8 @@ #include <jni.h> /* Header for class hdf_hdf5lib_H5_H5F */ -#ifndef _Included_hdf_hdf5lib_H5_H5F -#define _Included_hdf_hdf5lib_H5_H5F +#ifndef Included_hdf_hdf5lib_H5_H5F +#define Included_hdf_hdf5lib_H5_H5F #ifdef __cplusplus extern "C" { @@ -237,4 +236,4 @@ JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Fset_1libver_1bounds(JNIEnv *, jcla } /* end extern "C" */ #endif /* __cplusplus */ -#endif /* _Included_hdf_hdf5lib_H5_H5F */ +#endif /* Included_hdf_hdf5lib_H5_H5F */ diff --git a/java/src/jni/h5gImp.c b/java/src/jni/h5gImp.c index 43a6122..a0011d8 100644 --- a/java/src/jni/h5gImp.c +++ b/java/src/jni/h5gImp.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/jni/h5gImp.h b/java/src/jni/h5gImp.h index 3de21b7..b7130ed 100644 --- a/java/src/jni/h5gImp.h +++ b/java/src/jni/h5gImp.h @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -14,8 +13,8 @@ #include <jni.h> /* Header for class hdf_hdf5lib_H5_H5G */ -#ifndef _Included_hdf_hdf5lib_H5_H5G -#define _Included_hdf_hdf5lib_H5_H5G +#ifndef Included_hdf_hdf5lib_H5_H5G +#define Included_hdf_hdf5lib_H5_H5G #ifdef __cplusplus extern "C" { @@ -97,4 +96,4 @@ JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Grefresh(JNIEnv *, jclass, jlong); } /* end extern "C" */ #endif /* __cplusplus */ -#endif /* _Included_hdf_hdf5lib_H5_H5G */ +#endif /* Included_hdf_hdf5lib_H5_H5G */ diff --git a/java/src/jni/h5iImp.c b/java/src/jni/h5iImp.c index 78cc138..1e7821a 100644 --- a/java/src/jni/h5iImp.c +++ b/java/src/jni/h5iImp.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/jni/h5iImp.h b/java/src/jni/h5iImp.h index ff407d9..08d5fa1 100644 --- a/java/src/jni/h5iImp.h +++ b/java/src/jni/h5iImp.h @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -14,8 +13,8 @@ #include <jni.h> /* Header for class hdf_hdf5lib_H5_H5I */ -#ifndef _Included_hdf_hdf5lib_H5_H5I -#define _Included_hdf_hdf5lib_H5_H5I +#ifndef Included_hdf_hdf5lib_H5_H5I +#define Included_hdf_hdf5lib_H5_H5I #ifdef __cplusplus extern "C" { @@ -131,4 +130,4 @@ JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Idestroy_1type(JNIEnv *, jclass, ji } /* end extern "C" */ #endif /* __cplusplus */ -#endif /* _Included_hdf_hdf5lib_H5_H5I */ +#endif /* Included_hdf_hdf5lib_H5_H5I */ diff --git a/java/src/jni/h5jni.h b/java/src/jni/h5jni.h index 346b605..2c93846 100644 --- a/java/src/jni/h5jni.h +++ b/java/src/jni/h5jni.h @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -22,8 +21,8 @@ #include <string.h> #include "H5private.h" -#ifndef _Included_h5jni -#define _Included_h5jni +#ifndef Included_h5jni +#define Included_h5jni #ifdef __cplusplus #define ENVPTR (env) @@ -267,9 +266,10 @@ extern jboolean h5JNIFatalError(JNIEnv *env, const char *); extern jboolean h5nullArgument(JNIEnv *env, const char *); extern jboolean h5badArgument(JNIEnv *env, const char *); extern jboolean h5outOfMemory(JNIEnv *env, const char *); +extern jboolean h5assertion(JNIEnv *env, const char *); +extern jboolean h5unimplemented(JNIEnv *env, const char *); extern jboolean h5libraryError(JNIEnv *env); extern jboolean h5raiseException(JNIEnv *env, const char *, const char *); -extern jboolean h5unimplemented(JNIEnv *env, const char *functName); /* * The following macros are to facilitate immediate cleanup+return @@ -305,21 +305,27 @@ extern jboolean h5unimplemented(JNIEnv *env, const char *functName); goto done; \ } while (0) -#define H5_LIBRARY_ERROR(env) \ +#define H5_ASSERTION_ERROR(env, message) \ do { \ - h5libraryError(env); \ + h5assertion(env, message); \ goto done; \ } while (0) -#define H5_RAISE_EXCEPTION(env, message, exception) \ +#define H5_UNIMPLEMENTED(env, message) \ do { \ - h5raiseException(env, message, exception); \ + h5unimplemented(env, message); \ goto done; \ } while (0) -#define H5_UNIMPLEMENTED(env, message) \ +#define H5_LIBRARY_ERROR(env) \ do { \ - h5unimplemented(env, message); \ + h5libraryError(env); \ + goto done; \ + } while (0) + +#define H5_RAISE_EXCEPTION(env, message, exception) \ + do { \ + h5raiseException(env, message, exception); \ goto done; \ } while (0) @@ -338,4 +344,4 @@ extern jobject create_H5O_token_t(JNIEnv *env, const H5O_token_t *token, hbool_t } /* end extern "C" */ #endif /* __cplusplus */ -#endif /* _Included_h5jni */ +#endif /* Included_h5jni */ diff --git a/java/src/jni/h5lImp.c b/java/src/jni/h5lImp.c index a0b164a..43db4e9 100644 --- a/java/src/jni/h5lImp.c +++ b/java/src/jni/h5lImp.c @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -676,7 +675,7 @@ H5L_iterate_cb(hid_t g_id, const char *name, const H5L_info2_t *info, void *cb_d jobject visit_callback = wrapper->visit_callback; jstring str; JNIEnv * cbenv = NULL; - jclass cls; + jclass cbcls; jvalue args[5]; void * op_data = (void *)wrapper->op_data; jint status = -1; @@ -687,10 +686,10 @@ H5L_iterate_cb(hid_t g_id, const char *name, const H5L_info2_t *info, void *cb_d } /* Get the Method ID for the "callback" function of the H5L_iterate_t class */ - if (NULL == (cls = CBENVPTR->GetObjectClass(CBENVONLY, visit_callback))) + if (NULL == (cbcls = CBENVPTR->GetObjectClass(CBENVONLY, visit_callback))) CHECK_JNI_EXCEPTION(CBENVONLY, JNI_FALSE); - if (NULL == (mid = CBENVPTR->GetMethodID(CBENVONLY, cls, "callback", + if (NULL == (mid = CBENVPTR->GetMethodID(CBENVONLY, cbcls, "callback", "(JLjava/lang/String;Lhdf/hdf5lib/structs/H5L_info_t;Lhdf/" "hdf5lib/callbacks/H5L_iterate_opdata_t;)I"))) CHECK_JNI_EXCEPTION(CBENVONLY, JNI_FALSE); diff --git a/java/src/jni/h5lImp.h b/java/src/jni/h5lImp.h index 7a93c71..85aff03 100644 --- a/java/src/jni/h5lImp.h +++ b/java/src/jni/h5lImp.h @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -14,8 +13,8 @@ #include <jni.h> /* Header for class hdf_hdf5lib_H5_H5_H5L */ -#ifndef _Included_hdf_hdf5lib_H5_H5L -#define _Included_hdf_hdf5lib_H5_H5L +#ifndef Included_hdf_hdf5lib_H5_H5L +#define Included_hdf_hdf5lib_H5_H5L #ifdef __cplusplus extern "C" { @@ -171,4 +170,4 @@ JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Lunregister(JNIEnv *, jclass, jint) } /* end extern "C" */ #endif /* __cplusplus */ -#endif /* _Included_hdf_hdf5lib_H5_H5L */ +#endif /* Included_hdf_hdf5lib_H5_H5L */ diff --git a/java/src/jni/h5oImp.c b/java/src/jni/h5oImp.c index 1337456..3037bc6 100644 --- a/java/src/jni/h5oImp.c +++ b/java/src/jni/h5oImp.c @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -559,7 +558,7 @@ H5O_iterate_cb(hid_t g_id, const char *name, const H5O_info2_t *info, void *cb_d jobject token; jstring str; JNIEnv * cbenv = NULL; - jclass cls; + jclass cbcls; jvalue args[12]; void * op_data = (void *)wrapper->op_data; jint status = FAIL; @@ -569,10 +568,10 @@ H5O_iterate_cb(hid_t g_id, const char *name, const H5O_info2_t *info, void *cb_d H5_JNI_FATAL_ERROR(CBENVONLY, "H5O_iterate_cb: failed to attach current thread to JVM"); } - if (NULL == (cls = CBENVPTR->GetObjectClass(CBENVONLY, visit_callback))) + if (NULL == (cbcls = CBENVPTR->GetObjectClass(CBENVONLY, visit_callback))) CHECK_JNI_EXCEPTION(CBENVONLY, JNI_FALSE); - if (NULL == (mid = CBENVPTR->GetMethodID(CBENVONLY, cls, "callback", + if (NULL == (mid = CBENVPTR->GetMethodID(CBENVONLY, cbcls, "callback", "(JLjava/lang/String;Lhdf/hdf5lib/structs/H5O_info_t;Lhdf/" "hdf5lib/callbacks/H5O_iterate_opdata_t;)I"))) CHECK_JNI_EXCEPTION(CBENVONLY, JNI_FALSE); diff --git a/java/src/jni/h5oImp.h b/java/src/jni/h5oImp.h index 965df19..a7d7f31 100644 --- a/java/src/jni/h5oImp.h +++ b/java/src/jni/h5oImp.h @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -14,8 +13,8 @@ #include <jni.h> /* Header for class hdf_hdf5lib_H5_H5_H5O */ -#ifndef _Included_hdf_hdf5lib_H5_H5O -#define _Included_hdf_hdf5lib_H5_H5O +#ifndef Included_hdf_hdf5lib_H5_H5O +#define Included_hdf_hdf5lib_H5_H5O #ifdef __cplusplus extern "C" { @@ -218,4 +217,4 @@ JNIEXPORT jboolean JNICALL Java_hdf_hdf5lib_H5_H5Oare_1mdc_1flushes_1disabled(JN } /* end extern "C" */ #endif /* __cplusplus */ -#endif /* _Included_hdf_hdf5lib_H5_H5O */ +#endif /* Included_hdf_hdf5lib_H5_H5O */ diff --git a/java/src/jni/h5pACPLImp.c b/java/src/jni/h5pACPLImp.c index f6c14e1..6290e0e 100644 --- a/java/src/jni/h5pACPLImp.c +++ b/java/src/jni/h5pACPLImp.c @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/jni/h5pACPLImp.h b/java/src/jni/h5pACPLImp.h index 194afc0..15fcf33 100644 --- a/java/src/jni/h5pACPLImp.h +++ b/java/src/jni/h5pACPLImp.h @@ -1,18 +1,17 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -#ifndef _Included_hdf_hdf5lib_H5_H5PACPL -#define _Included_hdf_hdf5lib_H5_H5PACPL +#ifndef Included_hdf_hdf5lib_H5_H5PACPL +#define Included_hdf_hdf5lib_H5_H5PACPL #include <jni.h> @@ -24,4 +23,4 @@ extern "C" { } /* end extern "C" */ #endif /* __cplusplus */ -#endif /* _Included_hdf_hdf5lib_H5_H5PACPL */ +#endif /* Included_hdf_hdf5lib_H5_H5PACPL */ diff --git a/java/src/jni/h5pDAPLImp.c b/java/src/jni/h5pDAPLImp.c index 4654aa3..82802b9 100644 --- a/java/src/jni/h5pDAPLImp.c +++ b/java/src/jni/h5pDAPLImp.c @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/jni/h5pDAPLImp.h b/java/src/jni/h5pDAPLImp.h index 85238e1..bf11fef 100644 --- a/java/src/jni/h5pDAPLImp.h +++ b/java/src/jni/h5pDAPLImp.h @@ -1,18 +1,17 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -#ifndef _Included_hdf_hdf5lib_H5_H5PDAPL -#define _Included_hdf_hdf5lib_H5_H5PDAPL +#ifndef Included_hdf_hdf5lib_H5_H5PDAPL +#define Included_hdf_hdf5lib_H5_H5PDAPL #include <jni.h> @@ -94,4 +93,4 @@ JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5_H5Pget_1virtual_1printf_1gap(JNIEnv } /* end extern "C" */ #endif /* __cplusplus */ -#endif /* _Included_hdf_hdf5lib_H5_H5PDAPL */ +#endif /* Included_hdf_hdf5lib_H5_H5PDAPL */ diff --git a/java/src/jni/h5pDCPLImp.c b/java/src/jni/h5pDCPLImp.c index df9c4eb..760a5a8 100644 --- a/java/src/jni/h5pDCPLImp.c +++ b/java/src/jni/h5pDCPLImp.c @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/jni/h5pDCPLImp.h b/java/src/jni/h5pDCPLImp.h index 3a6a088..46d1cc3 100644 --- a/java/src/jni/h5pDCPLImp.h +++ b/java/src/jni/h5pDCPLImp.h @@ -1,18 +1,17 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -#ifndef _Included_hdf_hdf5lib_H5_H5PDCPL -#define _Included_hdf_hdf5lib_H5_H5PDCPL +#ifndef Included_hdf_hdf5lib_H5_H5PDCPL +#define Included_hdf_hdf5lib_H5_H5PDCPL #include <jni.h> @@ -321,4 +320,4 @@ JNIEXPORT jstring JNICALL Java_hdf_hdf5lib_H5_H5Pget_1virtual_1prefix(JNIEnv *, } /* end extern "C" */ #endif /* __cplusplus */ -#endif /* _Included_hdf_hdf5lib_H5_H5PDCPL */ +#endif /* Included_hdf_hdf5lib_H5_H5PDCPL */ diff --git a/java/src/jni/h5pDXPLImp.c b/java/src/jni/h5pDXPLImp.c index f7f9f96..c555d53 100644 --- a/java/src/jni/h5pDXPLImp.c +++ b/java/src/jni/h5pDXPLImp.c @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/jni/h5pDXPLImp.h b/java/src/jni/h5pDXPLImp.h index 9793ce7..21c40c4 100644 --- a/java/src/jni/h5pDXPLImp.h +++ b/java/src/jni/h5pDXPLImp.h @@ -1,18 +1,17 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -#ifndef _Included_hdf_hdf5lib_H5_H5PDXPL -#define _Included_hdf_hdf5lib_H5_H5PDXPL +#ifndef Included_hdf_hdf5lib_H5_H5PDXPL +#define Included_hdf_hdf5lib_H5_H5PDXPL #include <jni.h> @@ -182,4 +181,4 @@ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Pget_1btree_1ratios(JNIEnv *, jclas } /* end extern "C" */ #endif /* __cplusplus */ -#endif /* _Included_hdf_hdf5lib_H5_H5PDXPL */ +#endif /* Included_hdf_hdf5lib_H5_H5PDXPL */ diff --git a/java/src/jni/h5pFAPLImp.c b/java/src/jni/h5pFAPLImp.c index bbeddaf..ad85aae 100644 --- a/java/src/jni/h5pFAPLImp.c +++ b/java/src/jni/h5pFAPLImp.c @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -1364,6 +1363,76 @@ done: /* * Class: hdf_hdf5lib_H5 + * Method: H5Pset_file_locking + * Signature: (JZZ)V + */ +JNIEXPORT void JNICALL +Java_hdf_hdf5lib_H5_H5Pset_1file_1locking(JNIEnv *env, jclass clss, jlong fapl_id, jboolean use_file_locking, + jboolean ignore_when_disabled) +{ + hbool_t use_file_locking_val = TRUE; + hbool_t ignore_when_disabled_val = TRUE; + + UNUSED(clss); + + use_file_locking_val = (use_file_locking == JNI_TRUE) ? TRUE : FALSE; + ignore_when_disabled_val = (ignore_when_disabled == JNI_TRUE) ? TRUE : FALSE; + + if (H5Pset_file_locking((hid_t)fapl_id, use_file_locking_val, ignore_when_disabled_val) < 0) + H5_LIBRARY_ERROR(ENVONLY); + +done: + return; +} /* end Java_hdf_hdf5lib_H5_H5Pset_1file_1locking */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Pget_use_file_locking + * Signature: (J)Z + */ +JNIEXPORT jboolean JNICALL +Java_hdf_hdf5lib_H5_H5Pget_1use_1file_1locking(JNIEnv *env, jclass clss, jlong fapl_id) +{ + hbool_t use_file_locking_val = TRUE; + hbool_t unused = TRUE; + jboolean bval = JNI_FALSE; + + UNUSED(clss); + + if (H5Pget_file_locking((hid_t)fapl_id, &use_file_locking_val, &unused) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + bval = (use_file_locking_val == TRUE) ? JNI_TRUE : JNI_FALSE; + +done: + return bval; +} /* end Java_hdf_hdf5lib_H5_H5Pget_1use_1file_1locking */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Pget_ignore_disabled_file_locking + * Signature: (J)Z + */ +JNIEXPORT jboolean JNICALL +Java_hdf_hdf5lib_H5_H5Pget_1ignore_1disabled_1file_1locking(JNIEnv *env, jclass clss, jlong fapl_id) +{ + hbool_t ignore_when_disabled_val = TRUE; + hbool_t unused = TRUE; + jboolean bval = JNI_FALSE; + + UNUSED(clss); + + if (H5Pget_file_locking((hid_t)fapl_id, &unused, &ignore_when_disabled_val) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + bval = (ignore_when_disabled_val == TRUE) ? JNI_TRUE : JNI_FALSE; + +done: + return bval; +} /* end Java_hdf_hdf5lib_H5_H5Pget_1ignore_1disabled_1file_1locking */ + +/* + * Class: hdf_hdf5lib_H5 * Method: H5Pset_metadata_read_attempts * Signature: (JJ)V */ diff --git a/java/src/jni/h5pFAPLImp.h b/java/src/jni/h5pFAPLImp.h index 8c9d7ab..3c5988f 100644 --- a/java/src/jni/h5pFAPLImp.h +++ b/java/src/jni/h5pFAPLImp.h @@ -1,18 +1,17 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -#ifndef _Included_hdf_hdf5lib_H5_H5PFAPL -#define _Included_hdf_hdf5lib_H5_H5PFAPL +#ifndef Included_hdf_hdf5lib_H5_H5PFAPL +#define Included_hdf_hdf5lib_H5_H5PFAPL #include <jni.h> @@ -331,6 +330,32 @@ JNIEXPORT jboolean JNICALL Java_hdf_hdf5lib_H5_H5Pget_1evict_1on_1close(JNIEnv * /* * Class: hdf_hdf5lib_H5 + * Method: H5Pset_file_locking + * Signature: (JZZ)V + */ +JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Pset_1file_1locking(JNIEnv *env, jclass clss, jlong fapl_id, + jboolean use_file_locking, + jboolean ignore_when_disabled); + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Pget_use_file_locking + * Signature: (J)Z + */ +JNIEXPORT jboolean JNICALL Java_hdf_hdf5lib_H5_H5Pget_1use_1file_1locking(JNIEnv *env, jclass clss, + jlong fapl_id); + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Pget_ignore_disabled_file_locking + * Signature: (J)Z + */ +JNIEXPORT jboolean JNICALL Java_hdf_hdf5lib_H5_H5Pget_1ignore_1disabled_1file_1locking(JNIEnv *env, + jclass clss, + jlong fapl_id); + +/* + * Class: hdf_hdf5lib_H5 * Method: H5Pset_metadata_read_attempts * Signature: (JJ)V */ @@ -451,4 +476,4 @@ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Pget_1libver_1bounds(JNIEnv *, jcla } /* end extern "C" */ #endif /* __cplusplus */ -#endif /* _Included_hdf_hdf5lib_H5_H5PFAPL */ +#endif /* Included_hdf_hdf5lib_H5_H5PFAPL */ diff --git a/java/src/jni/h5pFCPLImp.c b/java/src/jni/h5pFCPLImp.c index fcb590e..ded3248 100644 --- a/java/src/jni/h5pFCPLImp.c +++ b/java/src/jni/h5pFCPLImp.c @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/jni/h5pFCPLImp.h b/java/src/jni/h5pFCPLImp.h index 924e325..94411d6 100644 --- a/java/src/jni/h5pFCPLImp.h +++ b/java/src/jni/h5pFCPLImp.h @@ -1,18 +1,17 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -#ifndef _Included_hdf_hdf5lib_H5_H5PFCPL -#define _Included_hdf_hdf5lib_H5_H5PFCPL +#ifndef Included_hdf_hdf5lib_H5_H5PFCPL +#define Included_hdf_hdf5lib_H5_H5PFCPL #include <jni.h> @@ -171,4 +170,4 @@ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Pget_1shared_1mesg_1phase_1change(J } /* end extern "C" */ #endif /* __cplusplus */ -#endif /* _Included_hdf_hdf5lib_H5_H5PFCPL */ +#endif /* Included_hdf_hdf5lib_H5_H5PFCPL */ diff --git a/java/src/jni/h5pGAPLImp.c b/java/src/jni/h5pGAPLImp.c index 9540387..b92e180 100644 --- a/java/src/jni/h5pGAPLImp.c +++ b/java/src/jni/h5pGAPLImp.c @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/jni/h5pGAPLImp.h b/java/src/jni/h5pGAPLImp.h index 73ad4a8..9091ff8 100644 --- a/java/src/jni/h5pGAPLImp.h +++ b/java/src/jni/h5pGAPLImp.h @@ -1,18 +1,17 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -#ifndef _Included_hdf_hdf5lib_H5_H5PGAPL -#define _Included_hdf_hdf5lib_H5_H5PGAPL +#ifndef Included_hdf_hdf5lib_H5_H5PGAPL +#define Included_hdf_hdf5lib_H5_H5PGAPL #include <jni.h> @@ -24,4 +23,4 @@ extern "C" { } /* end extern "C" */ #endif /* __cplusplus */ -#endif /* _Included_hdf_hdf5lib_H5_H5PGAPL */ +#endif /* Included_hdf_hdf5lib_H5_H5PGAPL */ diff --git a/java/src/jni/h5pGCPLImp.c b/java/src/jni/h5pGCPLImp.c index 67af902..2ba140d 100644 --- a/java/src/jni/h5pGCPLImp.c +++ b/java/src/jni/h5pGCPLImp.c @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/jni/h5pGCPLImp.h b/java/src/jni/h5pGCPLImp.h index 920e799..5090c3a 100644 --- a/java/src/jni/h5pGCPLImp.h +++ b/java/src/jni/h5pGCPLImp.h @@ -1,18 +1,17 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -#ifndef _Included_hdf_hdf5lib_H5_H5PGCPL -#define _Included_hdf_hdf5lib_H5_H5PGCPL +#ifndef Included_hdf_hdf5lib_H5_H5PGCPL +#define Included_hdf_hdf5lib_H5_H5PGCPL #include <jni.h> @@ -80,4 +79,4 @@ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Pget_1link_1phase_1change(JNIEnv *, } /* end extern "C" */ #endif /* __cplusplus */ -#endif /* _Included_hdf_hdf5lib_H5_H5PGCPL */ +#endif /* Included_hdf_hdf5lib_H5_H5PGCPL */ diff --git a/java/src/jni/h5pImp.c b/java/src/jni/h5pImp.c index 4ab359a..175794d 100644 --- a/java/src/jni/h5pImp.c +++ b/java/src/jni/h5pImp.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/jni/h5pImp.h b/java/src/jni/h5pImp.h index b35bf94..189e9d7 100644 --- a/java/src/jni/h5pImp.h +++ b/java/src/jni/h5pImp.h @@ -1,20 +1,19 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /* Header for class hdf_hdf5lib_H5_H5_H5P */ -#ifndef _Included_hdf_hdf5lib_H5_H5P -#define _Included_hdf_hdf5lib_H5_H5P +#ifndef Included_hdf_hdf5lib_H5_H5P +#define Included_hdf_hdf5lib_H5_H5P #include <jni.h> @@ -211,4 +210,4 @@ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5__1H5Pclose_1class(JNIEnv *, jclass, j } /* end extern "C" */ #endif /* __cplusplus */ -#endif /* _Included_hdf_hdf5lib_H5_H5P */ +#endif /* Included_hdf_hdf5lib_H5_H5P */ diff --git a/java/src/jni/h5pLAPLImp.c b/java/src/jni/h5pLAPLImp.c index 01b2bb1..1db495c 100644 --- a/java/src/jni/h5pLAPLImp.c +++ b/java/src/jni/h5pLAPLImp.c @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/jni/h5pLAPLImp.h b/java/src/jni/h5pLAPLImp.h index c08e0c9..8ddc8d2 100644 --- a/java/src/jni/h5pLAPLImp.h +++ b/java/src/jni/h5pLAPLImp.h @@ -1,18 +1,17 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -#ifndef _Included_hdf_hdf5lib_H5_H5PLAPL -#define _Included_hdf_hdf5lib_H5_H5PLAPL +#ifndef Included_hdf_hdf5lib_H5_H5PLAPL +#define Included_hdf_hdf5lib_H5_H5PLAPL #include <jni.h> @@ -88,4 +87,4 @@ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Pget_1elink_1acc_1flags(JNIEnv *, j } /* end extern "C" */ #endif /* __cplusplus */ -#endif /* _Included_hdf_hdf5lib_H5_H5PLAPL */ +#endif /* Included_hdf_hdf5lib_H5_H5PLAPL */ diff --git a/java/src/jni/h5pLCPLImp.c b/java/src/jni/h5pLCPLImp.c index 7c79796..b5eebd1 100644 --- a/java/src/jni/h5pLCPLImp.c +++ b/java/src/jni/h5pLCPLImp.c @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/jni/h5pLCPLImp.h b/java/src/jni/h5pLCPLImp.h index 009d1b4..4cdf6cd 100644 --- a/java/src/jni/h5pLCPLImp.h +++ b/java/src/jni/h5pLCPLImp.h @@ -1,18 +1,17 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -#ifndef _Included_hdf_hdf5lib_H5_H5PLCPL -#define _Included_hdf_hdf5lib_H5_H5PLCPL +#ifndef Included_hdf_hdf5lib_H5_H5PLCPL +#define Included_hdf_hdf5lib_H5_H5PLCPL #include <jni.h> @@ -24,4 +23,4 @@ extern "C" { } /* end extern "C" */ #endif /* __cplusplus */ -#endif /* _Included_hdf_hdf5lib_H5_H5PLCPL */ +#endif /* Included_hdf_hdf5lib_H5_H5PLCPL */ diff --git a/java/src/jni/h5pOCPLImp.c b/java/src/jni/h5pOCPLImp.c index 68fe471..bdcba46 100644 --- a/java/src/jni/h5pOCPLImp.c +++ b/java/src/jni/h5pOCPLImp.c @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/jni/h5pOCPLImp.h b/java/src/jni/h5pOCPLImp.h index ad45ab9..94d397b 100644 --- a/java/src/jni/h5pOCPLImp.h +++ b/java/src/jni/h5pOCPLImp.h @@ -1,18 +1,17 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -#ifndef _Included_hdf_hdf5lib_H5_H5POCPL -#define _Included_hdf_hdf5lib_H5_H5POCPL +#ifndef Included_hdf_hdf5lib_H5_H5POCPL +#define Included_hdf_hdf5lib_H5_H5POCPL #include <jni.h> @@ -81,4 +80,4 @@ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Pget_1attr_1creation_1order(JNIEnv } /* end extern "C" */ #endif /* __cplusplus */ -#endif /* _Included_hdf_hdf5lib_H5_H5POCPL */ +#endif /* Included_hdf_hdf5lib_H5_H5POCPL */ diff --git a/java/src/jni/h5pOCpyPLImp.c b/java/src/jni/h5pOCpyPLImp.c index 81664ce..b525b68 100644 --- a/java/src/jni/h5pOCpyPLImp.c +++ b/java/src/jni/h5pOCpyPLImp.c @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/jni/h5pOCpyPLImp.h b/java/src/jni/h5pOCpyPLImp.h index 662fba1..50ee972 100644 --- a/java/src/jni/h5pOCpyPLImp.h +++ b/java/src/jni/h5pOCpyPLImp.h @@ -1,18 +1,17 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -#ifndef _Included_hdf_hdf5lib_H5_H5POCpyPL -#define _Included_hdf_hdf5lib_H5_H5POCpyPL +#ifndef Included_hdf_hdf5lib_H5_H5POCpyPL +#define Included_hdf_hdf5lib_H5_H5POCpyPL #include <jni.h> @@ -54,4 +53,4 @@ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Pget_1copy_1object(JNIEnv *, jclass } /* end extern "C" */ #endif /* __cplusplus */ -#endif /* _Included_hdf_hdf5lib_H5_H5POCpyPL */ +#endif /* Included_hdf_hdf5lib_H5_H5POCpyPL */ diff --git a/java/src/jni/h5pStrCPLImp.c b/java/src/jni/h5pStrCPLImp.c index aceeb0b..a056e3a 100644 --- a/java/src/jni/h5pStrCPLImp.c +++ b/java/src/jni/h5pStrCPLImp.c @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/jni/h5pStrCPLImp.h b/java/src/jni/h5pStrCPLImp.h index 1e89314..c0a7ec2 100644 --- a/java/src/jni/h5pStrCPLImp.h +++ b/java/src/jni/h5pStrCPLImp.h @@ -1,18 +1,17 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -#ifndef _Included_hdf_hdf5lib_H5_H5PStrCPL -#define _Included_hdf_hdf5lib_H5_H5PStrCPL +#ifndef Included_hdf_hdf5lib_H5_H5PStrCPL +#define Included_hdf_hdf5lib_H5_H5PStrCPL #include <jni.h> @@ -38,4 +37,4 @@ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Pget_1char_1encoding(JNIEnv *, jcla } /* end extern "C" */ #endif /* __cplusplus */ -#endif /* _Included_hdf_hdf5lib_H5_H5PStrCPL */ +#endif /* Included_hdf_hdf5lib_H5_H5PStrCPL */ diff --git a/java/src/jni/h5plImp.c b/java/src/jni/h5plImp.c index 4d2743a..9193028 100644 --- a/java/src/jni/h5plImp.c +++ b/java/src/jni/h5plImp.c @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/jni/h5plImp.h b/java/src/jni/h5plImp.h index 82b0699..410a34f 100644 --- a/java/src/jni/h5plImp.h +++ b/java/src/jni/h5plImp.h @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -14,8 +13,8 @@ #include <jni.h> /* Header for class hdf_hdf5lib_H5_H5PL */ -#ifndef _Included_hdf_hdf5lib_H5_H5PL -#define _Included_hdf_hdf5lib_H5_H5PL +#ifndef Included_hdf_hdf5lib_H5_H5PL +#define Included_hdf_hdf5lib_H5_H5PL #ifdef __cplusplus extern "C" { @@ -88,4 +87,4 @@ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5PLsize(JNIEnv *, jclass); } /* end extern "C" */ #endif /* __cplusplus */ -#endif /* _Included_hdf_hdf5lib_H5_H5PL */ +#endif /* Included_hdf_hdf5lib_H5_H5PL */ diff --git a/java/src/jni/h5rImp.c b/java/src/jni/h5rImp.c index abdd8a1..9fe0701 100644 --- a/java/src/jni/h5rImp.c +++ b/java/src/jni/h5rImp.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -336,7 +336,7 @@ done: * Signature: ([BJJ)J */ JNIEXPORT jlong JNICALL -Java_hdf_hdf5lib_H5_H5Ropen_1object(JNIEnv *env, jclass clss, jbyteArray ref, jlong rapl_id, jlong oapl_id) +Java_hdf_hdf5lib_H5__1H5Ropen_1object(JNIEnv *env, jclass clss, jbyteArray ref, jlong rapl_id, jlong oapl_id) { jboolean isCopy; jbyte * refBuf = NULL; @@ -371,7 +371,7 @@ done: * Signature: ([BJJ)J */ JNIEXPORT jlong JNICALL -Java_hdf_hdf5lib_H5_H5Ropen_1region(JNIEnv *env, jclass clss, jbyteArray ref, jlong rapl_id, jlong oapl_id) +Java_hdf_hdf5lib_H5__1H5Ropen_1region(JNIEnv *env, jclass clss, jbyteArray ref, jlong rapl_id, jlong oapl_id) { jboolean isCopy; jbyte * refBuf = NULL; @@ -406,7 +406,7 @@ done: * Signature: ([BJJ)J */ JNIEXPORT jlong JNICALL -Java_hdf_hdf5lib_H5_H5Ropen_1attr(JNIEnv *env, jclass clss, jbyteArray ref, jlong rapl_id, jlong aapl_id) +Java_hdf_hdf5lib_H5__1H5Ropen_1attr(JNIEnv *env, jclass clss, jbyteArray ref, jlong rapl_id, jlong aapl_id) { jboolean isCopy; jbyte * refBuf = NULL; diff --git a/java/src/jni/h5rImp.h b/java/src/jni/h5rImp.h index d0c5e3b..ffd7737 100644 --- a/java/src/jni/h5rImp.h +++ b/java/src/jni/h5rImp.h @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -14,8 +13,8 @@ #include <jni.h> /* Header for class hdf_hdf5lib_H5_H5R */ -#ifndef _Included_hdf_hdf5lib_H5_H5R -#define _Included_hdf_hdf5lib_H5_H5R +#ifndef Included_hdf_hdf5lib_H5_H5R +#define Included_hdf_hdf5lib_H5_H5R #ifdef __cplusplus extern "C" { @@ -79,21 +78,21 @@ JNIEXPORT jbyteArray JNICALL Java_hdf_hdf5lib_H5_H5Rcopy(JNIEnv *, jclass, jbyte * Method: H5Ropen_object * Signature: ([BJJ)J */ -JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5_H5Ropen_1object(JNIEnv *, jclass, jbyteArray, jlong, jlong); +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5__1H5Ropen_1object(JNIEnv *, jclass, jbyteArray, jlong, jlong); /* * Class: hdf_hdf5lib_H5 * Method: H5Ropen_region * Signature: ([BJJ)J */ -JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5_H5Ropen_1region(JNIEnv *, jclass, jbyteArray, jlong, jlong); +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5__1H5Ropen_1region(JNIEnv *, jclass, jbyteArray, jlong, jlong); /* * Class: hdf_hdf5lib_H5 * Method: H5Ropen_attr * Signature: ([BJJ)J */ -JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5_H5Ropen_1attr(JNIEnv *, jclass, jbyteArray, jlong, jlong); +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5__1H5Ropen_1attr(JNIEnv *, jclass, jbyteArray, jlong, jlong); /* * Class: hdf_hdf5lib_H5 @@ -175,4 +174,4 @@ JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5_H5Rget_1name(JNIEnv *, jclass, jlong } /* end extern "C" */ #endif /* __cplusplus */ -#endif /* _Included_hdf_hdf5lib_H5_H5R */ +#endif /* Included_hdf_hdf5lib_H5_H5R */ diff --git a/java/src/jni/h5sImp.c b/java/src/jni/h5sImp.c index 2a9cff5..c3a8460 100644 --- a/java/src/jni/h5sImp.c +++ b/java/src/jni/h5sImp.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -1340,6 +1340,389 @@ done: return; } /* end Java_hdf_hdf5lib_H5_H5Sget_1regular_1hyperslab */ +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Sselect_copy + * Signature: (JJ)V + */ +JNIEXPORT void JNICALL +Java_hdf_hdf5lib_H5_H5Sselect_1copy(JNIEnv *env, jclass clss, jlong dst_id, jlong src_id) +{ + herr_t status = FAIL; + + UNUSED(clss); + + if ((status = H5Sselect_copy((hid_t)dst_id, (hid_t)src_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + +done: + return; +} /* end Java_hdf_hdf5lib_H5_H5Sselect_1copy */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Sselect_shape_same + * Signature: (JJ)Z + */ +JNIEXPORT jboolean JNICALL +Java_hdf_hdf5lib_H5_H5Sselect_1shape_1same(JNIEnv *env, jclass clss, jlong space1_id, jlong space2_id) +{ + htri_t bval = JNI_FALSE; + + UNUSED(clss); + + if ((bval = H5Sselect_shape_same((hid_t)space1_id, (hid_t)space2_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + bval = (bval > 0) ? JNI_TRUE : JNI_FALSE; + +done: + return (jboolean)bval; +} /* end Java_hdf_hdf5lib_H5_H5Sselect_1shape_1same */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Sselect_adjust + * Signature: (J[J)V + */ +JNIEXPORT void JNICALL +Java_hdf_hdf5lib_H5_H5Sselect_1adjust(JNIEnv *env, jclass clss, jlong space_id, jlongArray offset) +{ + jboolean isCopy; + hssize_t *offst = NULL; + jlong * offsetP = NULL; + jsize offset_rank = -1; + int i, rank = -1; + herr_t status = FAIL; + + UNUSED(clss); + + if (space_id < 0) + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_adjust: invalid dataspace ID"); + + if ((rank = H5Sget_simple_extent_ndims(space_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + if (NULL == offset) { + offsetP = NULL; + offst = (hssize_t *)offsetP; + } + else { + if ((offset_rank = ENVPTR->GetArrayLength(ENVONLY, offset)) < 0) { + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_adjust: offset length < 0"); + } + + if (offset_rank != rank) + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_adjust: offset rank doesn't match dataspace rank!"); + + PIN_LONG_ARRAY(ENVONLY, offset, offsetP, &isCopy, "H5Sselect_adjust: offset not pinned"); + + if (NULL == (offst = (hssize_t *)HDmalloc((size_t)offset_rank * sizeof(hsize_t)))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Sselect_adjust: failed to allocate offset buffer"); + } + + if ((status = H5Sselect_adjust(space_id, (hssize_t *)offst)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + for (i = 0; i < offset_rank; i++) { + offsetP[i] = (jlong)offst[i]; + } /* end for */ + +done: + if (offst) + HDfree(offst); + if (offsetP) + UNPIN_LONG_ARRAY(ENVONLY, offset, offsetP, (status < 0) ? JNI_ABORT : 0); + + return; +} /* end Java_hdf_hdf5lib_H5_H5Sselect_1adjust */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Sselect_intersect_block + * Signature: (J[J[J)Z + */ +JNIEXPORT jboolean JNICALL +Java_hdf_hdf5lib_H5_H5Sselect_1intersect_1block(JNIEnv *env, jclass clss, jlong space_id, jlongArray start, + jlongArray end) +{ + htri_t bval = JNI_FALSE; + jboolean isCopy; + hsize_t *strt = NULL, *nd = NULL; + jlong * startP = NULL, *endP = NULL; + jsize start_rank = -1, end_rank = -1; + int i, rank = -1; + + UNUSED(clss); + + if (space_id < 0) + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_intersect_block: invalid dataspace ID"); + + if ((rank = H5Sget_simple_extent_ndims(space_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + if (NULL == start) { + startP = NULL; + strt = (hsize_t *)startP; + } + else { + if ((start_rank = ENVPTR->GetArrayLength(ENVONLY, start)) < 0) { + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_intersect_block: start length < 0"); + } + + if (start_rank != rank) + H5_BAD_ARGUMENT_ERROR(ENVONLY, + "H5Sselect_intersect_block: start rank doesn't match dataspace rank!"); + + PIN_LONG_ARRAY(ENVONLY, start, startP, &isCopy, "H5Sselect_intersect_block: start not pinned"); + + if (NULL == (strt = (hsize_t *)HDmalloc((size_t)start_rank * sizeof(hsize_t)))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Sselect_intersect_block: failed to allocate start buffer"); + } + + if (NULL == end) { + endP = NULL; + nd = (hsize_t *)endP; + } + else { + if ((end_rank = ENVPTR->GetArrayLength(ENVONLY, end)) < 0) { + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_intersect_block: end array length < 0"); + } + + if (end_rank != rank) + H5_BAD_ARGUMENT_ERROR(ENVONLY, + "H5Sselect_intersect_block: end rank doesn't match dataspace rank!"); + + PIN_LONG_ARRAY(ENVONLY, end, endP, &isCopy, "H5Sselect_intersect_block: end not pinned"); + + if (NULL == (nd = (hsize_t *)HDmalloc((size_t)end_rank * sizeof(hsize_t)))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Sselect_intersect_block: failed to allocate end buffer"); + } + + if ((bval = H5Sselect_intersect_block(space_id, (hsize_t *)strt, (hsize_t *)nd)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + bval = (bval > 0) ? JNI_TRUE : JNI_FALSE; + + for (i = 0; i < start_rank; i++) { + startP[i] = (jlong)strt[i]; + endP[i] = (jlong)nd[i]; + } /* end for */ + +done: + if (strt) + HDfree(strt); + if (startP) + UNPIN_LONG_ARRAY(ENVONLY, start, startP, (bval < 0) ? JNI_ABORT : 0); + if (nd) + HDfree(nd); + if (endP) + UNPIN_LONG_ARRAY(ENVONLY, end, endP, (bval < 0) ? JNI_ABORT : 0); + + return (jboolean)bval; +} /* end Java_hdf_hdf5lib_H5_H5Sselect_1intersect_1block */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Sselect_project_intersection + * Signature: (JJJ)J + */ +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_H5_H5Sselect_1project_1intersection(JNIEnv *env, jclass clss, jlong src_space_id, + jlong dst_space_id, jlong src_intersect_space_id) +{ + hid_t sid = H5I_INVALID_HID; + + UNUSED(clss); + + if ((sid = H5Sselect_project_intersection(src_space_id, dst_space_id, src_intersect_space_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + +done: + + return (jlong)sid; +} /* end Java_hdf_hdf5lib_H5_H5Sselect_1project_1intersection */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Scombine_hyperslab + * Signature: (JI[J[J[J[J)J + */ +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_H5_H5Scombine_1hyperslab(JNIEnv *env, jclass clss, jlong space_id, jint op, jlongArray start, + jlongArray stride, jlongArray count, jlongArray block) +{ + jboolean isCopy; + hsize_t *strt = NULL, *strd = NULL, *cnt = NULL, *blk = NULL; + hsize_t *lp = NULL; + jlong * startP = NULL, *strideP = NULL, *countP = NULL, *blockP = NULL; + jlong * jlp = NULL; + jsize start_rank, stride_rank, count_rank, block_rank; + int i; + hid_t sid = H5I_INVALID_HID; + + UNUSED(clss); + + if (NULL == start) + H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: start is NULL"); + if (NULL == count) + H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: count is NULL"); + + if ((start_rank = ENVPTR->GetArrayLength(ENVONLY, start)) < 0) { + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: start array length < 0"); + } + if ((count_rank = ENVPTR->GetArrayLength(ENVONLY, count)) < 0) { + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: count array length < 0"); + } + + if (start_rank != count_rank) + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: count and start have different rank!"); + + PIN_LONG_ARRAY(ENVONLY, start, startP, &isCopy, "H5Scombine_hyperslab: start not pinned"); + + if (NULL == (strt = lp = (hsize_t *)HDmalloc((size_t)start_rank * sizeof(hsize_t)))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Scombine_hyperslab: failed to allocate start buffer"); + + jlp = (jlong *)startP; + for (i = 0; i < start_rank; i++) { + *lp = (hsize_t)*jlp; + lp++; + jlp++; + } /* end if */ + + PIN_LONG_ARRAY(ENVONLY, count, countP, &isCopy, "H5Scombine_hyperslab: count not pinned"); + + if (NULL == (cnt = lp = (hsize_t *)HDmalloc((size_t)count_rank * sizeof(hsize_t)))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Scombine_hyperslab: failed to allocate count buffer"); + + jlp = (jlong *)countP; + for (i = 0; i < count_rank; i++) { + *lp = (hsize_t)*jlp; + lp++; + jlp++; + } /* end if */ + + if (NULL == stride) { + strideP = NULL; + strd = (hsize_t *)strideP; + } + else { + if ((stride_rank = ENVPTR->GetArrayLength(ENVONLY, stride)) < 0) { + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: stride array length < 0"); + } + + if (stride_rank != start_rank) + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: stride and start have different rank!"); + + PIN_LONG_ARRAY(ENVONLY, stride, strideP, &isCopy, "H5Scombine_hyperslab: stride not pinned"); + + if (NULL == (strd = lp = (hsize_t *)HDmalloc((size_t)stride_rank * sizeof(hsize_t)))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Scombine_hyperslab: failed to allocate stride buffer"); + + jlp = (jlong *)strideP; + for (i = 0; i < stride_rank; i++) { + *lp = (hsize_t)*jlp; + lp++; + jlp++; + } /* end if */ + } + + if (NULL == block) { + blockP = NULL; + blk = (hsize_t *)blockP; + } + else { + if ((block_rank = ENVPTR->GetArrayLength(ENVONLY, block)) < 0) { + CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE); + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: block array length < 0"); + } + + if (block_rank != start_rank) + H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Scombine_hyperslab: block and start have different rank!"); + + PIN_LONG_ARRAY(ENVONLY, block, blockP, &isCopy, "H5Scombine_hyperslab: block not pinned"); + + if (NULL == (blk = lp = (hsize_t *)HDmalloc((size_t)block_rank * sizeof(hsize_t)))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Scombine_hyperslab: failed to allocate block buffer"); + + jlp = (jlong *)blockP; + for (i = 0; i < block_rank; i++) { + *lp = (hsize_t)*jlp; + lp++; + jlp++; + } /* end for */ + } + + if ((sid = H5Scombine_hyperslab(space_id, (H5S_seloper_t)op, (const hsize_t *)strt, (const hsize_t *)strd, + (const hsize_t *)cnt, (const hsize_t *)blk)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + +done: + if (blk) + HDfree(blk); + if (blockP) + UNPIN_LONG_ARRAY(ENVONLY, block, blockP, JNI_ABORT); + if (strd) + HDfree(strd); + if (strideP) + UNPIN_LONG_ARRAY(ENVONLY, stride, strideP, JNI_ABORT); + if (cnt) + HDfree(cnt); + if (countP) + UNPIN_LONG_ARRAY(ENVONLY, count, countP, JNI_ABORT); + if (strt) + HDfree(strt); + if (startP) + UNPIN_LONG_ARRAY(ENVONLY, start, startP, JNI_ABORT); + + return (jlong)sid; +} /* end Java_hdf_hdf5lib_H5_H5Sselect_1hyperslab */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Smodify_select + * Signature: (JIJ)V + */ +JNIEXPORT void JNICALL +Java_hdf_hdf5lib_H5_H5Smodify_1select(JNIEnv *env, jclass clss, jlong space1_id, jint op, jlong space2_id) +{ + herr_t status = FAIL; + + UNUSED(clss); + + if ((status = H5Smodify_select((hid_t)space1_id, (H5S_seloper_t)op, (hid_t)space2_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + +done: + return; +} /* end Java_hdf_hdf5lib_H5_H5Smodify_1select */ + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Scombine_select + * Signature: (JIJ)J + */ +JNIEXPORT jlong JNICALL +Java_hdf_hdf5lib_H5_H5Scombine_1select(JNIEnv *env, jclass clss, jlong space1_id, jint op, jlong space2_id) +{ + hid_t sid = H5I_INVALID_HID; + + UNUSED(clss); + + if ((sid = H5Scombine_select((hid_t)space1_id, (H5S_seloper_t)op, (hid_t)space2_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + +done: + + return (jlong)sid; +} /* end Java_hdf_hdf5lib_H5_H5Scombine_1select */ + #ifdef __cplusplus } /* end extern "C" */ #endif /* __cplusplus */ diff --git a/java/src/jni/h5sImp.h b/java/src/jni/h5sImp.h index ee28b39..a758d5a 100644 --- a/java/src/jni/h5sImp.h +++ b/java/src/jni/h5sImp.h @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -14,8 +13,8 @@ #include <jni.h> /* Header for class hdf_hdf5lib_H5_H5S */ -#ifndef _Included_hdf_hdf5lib_H5_H5S -#define _Included_hdf_hdf5lib_H5_H5S +#ifndef Included_hdf_hdf5lib_H5_H5S +#define Included_hdf_hdf5lib_H5_H5S #ifdef __cplusplus extern "C" { @@ -259,8 +258,67 @@ JNIEXPORT jboolean JNICALL Java_hdf_hdf5lib_H5_H5Sis_1regular_1hyperslab(JNIEnv JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Sget_1regular_1hyperslab(JNIEnv *, jclass, jlong, jlongArray, jlongArray, jlongArray, jlongArray); +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Sselect_copy + * Signature: (JJ)V + */ +JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Sselect_1copy(JNIEnv *, jclass, jlong, jlong); + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Sselect_shape_same + * Signature: (JJ)Z + */ +JNIEXPORT jboolean JNICALL Java_hdf_hdf5lib_H5_H5Sselect_1shape_1same(JNIEnv *, jclass, jlong, jlong); + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Sselect_adjust + * Signature: (J[J)V + */ +JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Sselect_1adjust(JNIEnv *, jclass, jlong, jlongArray); + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Sselect_intersect_block + * Signature: (J[J[J)Z + */ +JNIEXPORT jboolean JNICALL Java_hdf_hdf5lib_H5_H5Sselect_1intersect_1block(JNIEnv *, jclass, jlong, + jlongArray, jlongArray); + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Sselect_project_intersection + * Signature: (JJJ)J + */ +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5_H5Sselect_1project_1intersection(JNIEnv *, jclass, jlong, jlong, + jlong); + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Scombine_hyperslab + * Signature: (JI[J[J[J[J)J + */ +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5_H5Scombine_1hyperslab(JNIEnv *, jclass, jlong, jint, jlongArray, + jlongArray, jlongArray, jlongArray); + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Smodify_select + * Signature: (JIJ)V + */ +JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Smodify_1select(JNIEnv *, jclass, jlong, jint, jlong); + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5Scombine_select + * Signature: (JIJ)J + */ +JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5_H5Scombine_1select(JNIEnv *, jclass, jlong, jint, jlong); + #ifdef __cplusplus } /* end extern "C" */ #endif /* __cplusplus */ -#endif /* _Included_hdf_hdf5lib_H5_H5S */ +#endif /* Included_hdf_hdf5lib_H5_H5S */ diff --git a/java/src/jni/h5tImp.c b/java/src/jni/h5tImp.c index e968ad2..8cd1afb 100644 --- a/java/src/jni/h5tImp.c +++ b/java/src/jni/h5tImp.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/jni/h5tImp.h b/java/src/jni/h5tImp.h index 41f7681..e671456 100644 --- a/java/src/jni/h5tImp.h +++ b/java/src/jni/h5tImp.h @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -14,8 +13,8 @@ #include <jni.h> /* Header for class hdf_hdf5lib_H5_H5T */ -#ifndef _Included_hdf_hdf5lib_H5_H5T -#define _Included_hdf_hdf5lib_H5_H5T +#ifndef Included_hdf_hdf5lib_H5_H5T +#define Included_hdf_hdf5lib_H5_H5T #ifdef __cplusplus extern "C" { @@ -506,4 +505,4 @@ JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Trefresh(JNIEnv *, jclass, jlong); } /* end extern "C" */ #endif /* __cplusplus */ -#endif /* _Included_hdf_hdf5lib_H5_H5T */ +#endif /* Included_hdf_hdf5lib_H5_H5T */ diff --git a/java/src/jni/h5util.c b/java/src/jni/h5util.c index eff6d5b..6281481 100644 --- a/java/src/jni/h5util.c +++ b/java/src/jni/h5util.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -28,8 +28,6 @@ extern "C" { #include "hdf5.h" #include "h5util.h" -#define SKIP_UNUSED_DUMP_ROUTINES - /* size of hyperslab buffer when a dataset is bigger than H5TOOLS_MALLOCSIZE */ hsize_t H5TOOLS_BUFSIZE = (32 * 1024 * 1024); /* 32 MB */ int H5TOOLS_TEXT_BLOCK = 16; /* Number of elements on a line in a text export file */ @@ -54,18 +52,21 @@ void * edata; /* Local Prototypes */ /********************/ -#ifndef SKIP_UNUSED_DUMP_ROUTINES -static int h5str_dump_region_blocks(JNIEnv *env, h5str_t *str, hid_t region, hid_t region_obj); -static int h5str_dump_region_points(JNIEnv *env, h5str_t *str, hid_t region, hid_t region_obj); -#endif +int h5str_region_dataset(JNIEnv *env, h5str_t *out_str, H5R_ref_t *ref_vp, int expand_data); + +static int h5str_dump_region_blocks(JNIEnv *env, h5str_t *str, hid_t region, hid_t region_obj, + int expand_data); +static int h5str_dump_region_points(JNIEnv *env, h5str_t *str, hid_t region, hid_t region_obj, + int expand_data); +static int h5str_dump_region_attribute(JNIEnv *env, h5str_t *str, hid_t region_id); static int h5str_is_zero(const void *_mem, size_t size); static hid_t h5str_get_native_type(hid_t type); static hid_t h5str_get_little_endian_type(hid_t type); static hid_t h5str_get_big_endian_type(hid_t type); static htri_t h5str_detect_vlen(hid_t tid); static htri_t h5str_detect_vlen_str(hid_t tid); -static int h5tools_dump_simple_data(JNIEnv *env, FILE *stream, hid_t container, hid_t type, void *_mem, - hsize_t nelmts); +static int h5str_dump_simple_data(JNIEnv *env, FILE *stream, hid_t container, hid_t type, void *_mem, + hsize_t nelmts); static int h5str_render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t block_nelmts); static int render_bin_output_region_data_blocks(FILE *stream, hid_t region_id, hid_t container, int ndims, @@ -185,13 +186,14 @@ h5str_convert(JNIEnv *env, char **in_str, hid_t container, hid_t tid, void *out_ H5T_class_t tclass = H5T_NO_CLASS; const char delimiter[] = " ," H5_COMPOUND_BEGIN_INDICATOR H5_COMPOUND_END_INDICATOR H5_ARRAY_BEGIN_INDICATOR H5_ARRAY_END_INDICATOR H5_VLEN_BEGIN_INDICATOR H5_VLEN_END_INDICATOR; - size_t typeSize = 0; - hid_t mtid = H5I_INVALID_HID; - char * this_str = NULL; - char * token; - char * cptr = NULL; - int n; - size_t retVal = 0; + + size_t retVal = 0; + size_t typeSize = 0; + hid_t mtid = H5I_INVALID_HID; + char * this_str = NULL; + char * cptr = NULL; + char * token; + int n; if (!in_str) H5_NULL_ARGUMENT_ERROR(ENVONLY, "h5str_convert: in_str is NULL"); @@ -239,7 +241,7 @@ h5str_convert(JNIEnv *env, char **in_str, hid_t container, hid_t tid, void *out_ case sizeof(long double): { long double tmp_ldouble = 0.0; - sscanf(token, "%Lf", &tmp_ldouble); + sscanf(token, "%Lg", &tmp_ldouble); HDmemcpy(cptr, &tmp_ldouble, sizeof(long double)); break; } @@ -644,27 +646,27 @@ done: * * Purpose: Object reference -- show the name of the referenced object. * - * Return: Nothing + * Return: SUCCEED or FAIL *------------------------------------------------------------------------- */ -void -h5str_sprint_reference(JNIEnv *env, h5str_t *out_str, hid_t container, void *ref_p) +int +h5str_sprint_reference(JNIEnv *env, h5str_t *out_str, void *ref_p) { - ssize_t buf_size; - char * ref_name = NULL; - const H5R_ref_t *ref_vp = (H5R_ref_t *)ref_p; + ssize_t buf_size; + char * ref_name = NULL; + H5R_ref_t *ref_vp = (H5R_ref_t *)ref_p; - UNUSED(container); + int ret_value = FAIL; if (!h5str_append(out_str, " \"")) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); buf_size = H5Rget_file_name(ref_vp, NULL, 0); if (buf_size) { ref_name = (char *)HDmalloc(sizeof(char) * (size_t)buf_size + 1); if (H5Rget_file_name(ref_vp, ref_name, buf_size + 1) >= 0) { ref_name[buf_size] = '\0'; if (!h5str_append(out_str, ref_name)) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); } HDfree(ref_name); ref_name = NULL; @@ -676,7 +678,7 @@ h5str_sprint_reference(JNIEnv *env, h5str_t *out_str, hid_t container, void *ref if (H5Rget_obj_name(ref_vp, H5P_DEFAULT, ref_name, buf_size + 1) >= 0) { ref_name[buf_size] = '\0'; if (!h5str_append(out_str, ref_name)) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); } HDfree(ref_name); ref_name = NULL; @@ -689,17 +691,61 @@ h5str_sprint_reference(JNIEnv *env, h5str_t *out_str, hid_t container, void *ref if (H5Rget_attr_name(ref_vp, ref_name, buf_size + 1) >= 0) { ref_name[buf_size] = '\0'; if (!h5str_append(out_str, ref_name)) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); } HDfree(ref_name); ref_name = NULL; } } if (!h5str_append(out_str, "\"")) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); + + ret_value = SUCCEED; done: if (ref_name) HDfree(ref_name); + + return ret_value; +} /* h5str_sprint_reference */ + +int +h5str_region_dataset(JNIEnv *env, h5str_t *out_str, H5R_ref_t *ref_vp, int expand_data) +{ + hid_t new_obj_id = H5I_INVALID_HID; + hid_t new_obj_sid = H5I_INVALID_HID; + H5S_sel_type region_type; + + int ret_value = FAIL; + + if ((new_obj_id = H5Ropen_object(ref_vp, H5P_DEFAULT, H5P_DEFAULT)) < 0) { + ret_value = SUCCEED; /* An uncreated region is a valid state */ + goto done; + } + + if ((new_obj_sid = H5Ropen_region(ref_vp, H5P_DEFAULT, H5P_DEFAULT)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + if ((region_type = H5Sget_select_type(new_obj_sid)) > H5S_SEL_ERROR) { + if (H5S_SEL_POINTS == region_type) { + if (h5str_dump_region_points(ENVONLY, out_str, new_obj_sid, new_obj_id, expand_data) < 0) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + } + else if (H5S_SEL_HYPERSLABS == region_type) { + if (h5str_dump_region_blocks(ENVONLY, out_str, new_obj_sid, new_obj_id, expand_data) < 0) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + } + } + + ret_value = SUCCEED; +done: + if (new_obj_sid >= 0) + if (H5Sclose(new_obj_sid) < 0) + H5_LIBRARY_ERROR(ENVONLY); + if (new_obj_id >= 0) + if (H5Dclose(new_obj_id) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + return ret_value; } /* @@ -710,8 +756,7 @@ done: * FAILURE: 0 */ size_t -h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *in_buf, size_t in_buf_len, - int expand_data) +h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *in_buf, int expand_data) { unsigned char *ucptr = (unsigned char *)in_buf; static char fmt_llong[8], fmt_ullong[8]; @@ -719,7 +764,6 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i size_t typeSize = 0; H5T_sign_t nsign = H5T_SGN_ERROR; hid_t mtid = H5I_INVALID_HID; - hid_t obj = H5I_INVALID_HID; char * cptr = (char *)in_buf; char * this_str = NULL; int n; @@ -734,8 +778,6 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i H5_LIBRARY_ERROR(ENVONLY); if (!(typeSize = H5Tget_size(tid))) H5_LIBRARY_ERROR(ENVONLY); - if (!(nsign = H5Tget_sign(tid))) - H5_LIBRARY_ERROR(ENVONLY); /* Build default formats for long long types */ if (!fmt_llong[0]) { @@ -744,7 +786,6 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i if (HDsnprintf(fmt_ullong, sizeof(fmt_ullong), "%%%su", H5_PRINTF_LL_WIDTH) < 0) H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); } /* end if */ - switch (tclass) { case H5T_FLOAT: { switch (typeSize) { @@ -784,7 +825,7 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i if (NULL == (this_str = (char *)HDmalloc(27))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); - if (HDsprintf(this_str, "%Lf", tmp_ldouble) < 0) + if (HDsprintf(this_str, "%Lg", tmp_ldouble) < 0) H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); break; @@ -805,6 +846,8 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i htri_t is_variable; char * tmp_str; + typeSize = 0; + if ((is_variable = H5Tis_variable_str(tid)) < 0) H5_LIBRARY_ERROR(ENVONLY); @@ -1003,7 +1046,7 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i H5_LIBRARY_ERROR(ENVONLY); if (!h5str_append(out_str, H5_COMPOUND_BEGIN_INDICATOR)) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); for (i = 0; i < (unsigned)n; i++) { offset = H5Tget_member_offset(tid, i); @@ -1011,12 +1054,12 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i if ((mtid = H5Tget_member_type(tid, i)) < 0) H5_LIBRARY_ERROR(ENVONLY); - if (!h5str_sprintf(ENVONLY, out_str, container, mtid, &cptr[offset], in_buf_len, expand_data)) + if (!h5str_sprintf(ENVONLY, out_str, container, mtid, &cptr[offset], expand_data)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); if ((i + 1) < (unsigned)n) if (!h5str_append(out_str, ", ")) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); if (H5Tclose(mtid) < 0) H5_LIBRARY_ERROR(ENVONLY); @@ -1024,7 +1067,7 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i } if (!h5str_append(out_str, H5_COMPOUND_END_INDICATOR)) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); break; } @@ -1034,7 +1077,7 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i if (H5Tenum_nameof(tid, cptr, enum_name, sizeof enum_name) >= 0) { if (!h5str_append(out_str, enum_name)) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); } else { size_t i; @@ -1057,124 +1100,112 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i } case H5T_REFERENCE: { - if (h5str_is_zero(cptr, typeSize)) { - if (!h5str_append(out_str, "NULL")) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - break; - } + /* H5T_STD_REF */ + hid_t new_obj_id = H5I_INVALID_HID; + H5O_type_t obj_type = -1; /* Object type */ + H5R_type_t ref_type; /* Reference type */ - if (H5Tequal(tid, H5T_STD_REF)) { - H5O_type_t obj_type = -1; /* Object type */ - H5R_type_t ref_type; /* Reference type */ - const H5R_ref_t *ref_vp = (H5R_ref_t *)cptr; + H5R_ref_t *ref_vp = (H5R_ref_t *)cptr; - ref_type = H5Rget_type(ref_vp); - H5Rget_obj_type3(ref_vp, H5P_DEFAULT, &obj_type); + ref_type = H5Rget_type(ref_vp); + if (!h5str_is_zero(ref_vp, H5Tget_size(H5T_STD_REF))) { switch (ref_type) { - case H5R_OBJECT1: { - /* Object references -- show the type and OID of the referenced object. */ - H5O_info2_t oi; - - if ((obj = H5Ropen_object(ref_vp, H5P_DEFAULT, H5P_DEFAULT)) >= 0) { - H5Oget_info3(obj, &oi, H5O_INFO_BASIC); - if (H5Oclose(obj) < 0) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + case H5R_OBJECT1: + if (H5Rget_obj_type3(ref_vp, H5P_DEFAULT, &obj_type) >= 0) { + switch (obj_type) { + case H5O_TYPE_DATASET: + if (h5str_region_dataset(ENVONLY, out_str, ref_vp, expand_data) < 0) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + break; + + case H5O_TYPE_GROUP: + case H5O_TYPE_NAMED_DATATYPE: + case H5O_TYPE_MAP: + case H5O_TYPE_UNKNOWN: + case H5O_TYPE_NTYPES: + default: { + /* Object references -- show the type and OID of the referenced object. */ + H5O_info2_t oi; + char * obj_tok_str = NULL; + if ((new_obj_id = H5Ropen_object(ref_vp, H5P_DEFAULT, H5P_DEFAULT)) >= + 0) { + H5Oget_info3(new_obj_id, &oi, H5O_INFO_BASIC); + H5Otoken_to_str(new_obj_id, &oi.token, &obj_tok_str); + if (H5Dclose(new_obj_id) < 0) + H5_LIBRARY_ERROR(ENVONLY); + } + else + H5_LIBRARY_ERROR(ENVONLY); + + if (NULL == (this_str = (char *)HDmalloc(14))) + H5_OUT_OF_MEMORY_ERROR( + ENVONLY, "h5str_sprintf: failed to allocate string buffer"); + if (HDsprintf(this_str, "%u-", (unsigned)oi.type) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (!h5str_append(out_str, this_str)) + H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); + HDfree(this_str); + this_str = NULL; + + /* Print OID */ + { + char *token_str; + + H5Otoken_to_str(tid, &oi.token, &token_str); + + if (NULL == (this_str = (char *)HDmalloc(64 + strlen(token_str) + 1))) + H5_OUT_OF_MEMORY_ERROR( + ENVONLY, "h5str_sprintf: failed to allocate string buffer"); + if (HDsprintf(this_str, "%lu:%s", oi.fileno, token_str) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + + H5free_memory(token_str); + } + } break; + } /* end switch */ } else - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - - if (NULL == (this_str = (char *)HDmalloc(14))) - H5_OUT_OF_MEMORY_ERROR(ENVONLY, - "h5str_sprintf: failed to allocate string buffer"); - if (HDsprintf(this_str, "%u-", (unsigned)oi.type) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); - if (!h5str_append(out_str, this_str)) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - HDfree(this_str); - this_str = NULL; - - switch (obj_type) { - case H5O_TYPE_GROUP: - if (!h5str_append(out_str, H5_TOOLS_GROUP)) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - break; - - case H5O_TYPE_DATASET: - if (!h5str_append(out_str, H5_TOOLS_DATASET)) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - break; - - case H5O_TYPE_NAMED_DATATYPE: - if (!h5str_append(out_str, H5_TOOLS_DATATYPE)) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - break; - - case H5O_TYPE_MAP: - case H5O_TYPE_UNKNOWN: - case H5O_TYPE_NTYPES: - default: - break; - } /* end switch */ - H5Oclose(obj); - h5str_sprint_reference(ENVONLY, out_str, container, ref_vp); - - /* Print OID */ - { - char *token_str; - - H5Otoken_to_str(tid, &oi.token, &token_str); - - if (NULL == (this_str = (char *)HDmalloc(64 + strlen(token_str) + 1))) - H5_OUT_OF_MEMORY_ERROR(ENVONLY, - "h5str_sprintf: failed to allocate string buffer"); - if (HDsprintf(this_str, "%lu:%s", oi.fileno, token_str) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); - - H5free_memory(token_str); - } - - } - - break; + H5_LIBRARY_ERROR(ENVONLY); + break; case H5R_DATASET_REGION1: - if (!h5str_append(out_str, H5_TOOLS_DATASET)) + if (h5str_region_dataset(ENVONLY, out_str, ref_vp, expand_data) < 0) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - h5str_sprint_reference(ENVONLY, out_str, container, (void *)cptr); break; case H5R_OBJECT2: - switch (obj_type) { - case H5O_TYPE_GROUP: - if (!h5str_append(out_str, H5_TOOLS_GROUP)) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - break; - - case H5O_TYPE_DATASET: - if (!h5str_append(out_str, H5_TOOLS_DATASET)) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - break; - - case H5O_TYPE_NAMED_DATATYPE: - if (!h5str_append(out_str, H5_TOOLS_DATATYPE)) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - break; - - case H5O_TYPE_MAP: - case H5O_TYPE_UNKNOWN: - case H5O_TYPE_NTYPES: - default: - break; - } /* end switch */ - h5str_sprint_reference(ENVONLY, out_str, container, (void *)cptr); + if (H5Rget_obj_type3(ref_vp, H5P_DEFAULT, &obj_type) >= 0) { + switch (obj_type) { + case H5O_TYPE_GROUP: + break; + + case H5O_TYPE_DATASET: + if (h5str_region_dataset(ENVONLY, out_str, ref_vp, expand_data) < 0) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + break; + + case H5O_TYPE_NAMED_DATATYPE: + break; + + case H5O_TYPE_MAP: + case H5O_TYPE_UNKNOWN: + case H5O_TYPE_NTYPES: + default: + break; + } /* end switch */ + } + else + H5_ASSERTION_ERROR(ENVONLY, "h5str_sprintf: H5R_OBJECT2 failed"); break; case H5R_DATASET_REGION2: - if (!h5str_append(out_str, H5_TOOLS_DATASET)) + if (h5str_region_dataset(ENVONLY, out_str, ref_vp, expand_data) < 0) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - h5str_sprint_reference(ENVONLY, out_str, container, (void *)cptr); break; case H5R_ATTR: - if (!h5str_append(out_str, H5_TOOLS_ATTRIBUTE)) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - h5str_sprint_reference(ENVONLY, out_str, container, (void *)cptr); + if ((new_obj_id = H5Ropen_attr(ref_vp, H5P_DEFAULT, H5P_DEFAULT)) >= 0) { + if (h5str_dump_region_attribute(ENVONLY, out_str, new_obj_id) < 0) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + if (H5Aclose(new_obj_id) < 0) + H5_LIBRARY_ERROR(ENVONLY); + } break; case H5R_BADTYPE: case H5R_MAXTYPE: @@ -1182,14 +1213,9 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i break; } /* end switch */ } - else if (H5Tequal(tid, H5T_STD_REF_DSETREG)) { - /* (H5R_DSET_REG_REF_BUF_SIZE == typeSize) */ - H5_LIBRARY_ERROR(ENVONLY); - } - else if (H5Tequal(tid, H5T_STD_REF_OBJ)) { - /* (H5R_OBJ_REF_BUF_SIZE == typeSize) */ + + if (H5Rdestroy(ref_vp) < 0) H5_LIBRARY_ERROR(ENVONLY); - } break; } @@ -1200,7 +1226,7 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i int rank = 0; if (!h5str_append(out_str, H5_ARRAY_BEGIN_INDICATOR)) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); if ((mtid = H5Tget_super(tid)) < 0) H5_LIBRARY_ERROR(ENVONLY); @@ -1218,17 +1244,16 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i total_elmts *= dims[i]; for (i = 0; i < total_elmts; i++) { - if (!h5str_sprintf(ENVONLY, out_str, container, mtid, &(cptr[i * baseSize]), in_buf_len, - expand_data)) + if (!h5str_sprintf(ENVONLY, out_str, container, mtid, &(cptr[i * baseSize]), expand_data)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); if ((i + 1) < total_elmts) if (!h5str_append(out_str, ", ")) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); } if (!h5str_append(out_str, H5_ARRAY_END_INDICATOR)) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); if (H5Tclose(mtid) < 0) H5_LIBRARY_ERROR(ENVONLY); @@ -1249,20 +1274,20 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i H5_LIBRARY_ERROR(ENVONLY); if (!h5str_append(out_str, H5_VLEN_BEGIN_INDICATOR)) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); for (i = 0; i < (unsigned)vl_buf->len; i++) { if (!h5str_sprintf(ENVONLY, out_str, container, mtid, &(((char *)vl_buf->p)[i * baseSize]), - vl_buf->len, expand_data)) + expand_data)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); if ((i + 1) < (unsigned)vl_buf->len) if (!h5str_append(out_str, ", ")) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); } if (!h5str_append(out_str, H5_VLEN_END_INDICATOR)) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); if (H5Tclose(mtid) < 0) H5_LIBRARY_ERROR(ENVONLY); @@ -1304,7 +1329,7 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i if (this_str) { if (!h5str_append(out_str, this_str)) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); HDfree(this_str); this_str = NULL; @@ -1405,12 +1430,12 @@ h5str_print_region_data_blocks(JNIEnv *env, hid_t region_id, h5str_t *str, int n for (numindex = 0; numindex < numelem; numindex++) { if (!h5str_sprintf(ENVONLY, str, region_id, type_id, ((char *)region_buf + numindex * type_size), - 0, 1)) + 1)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); if (numindex + 1 < numelem) if (!h5str_append(str, ", ")) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); } /* end for (jndx = 0; jndx < numelem; jndx++, region_elmtno++, ctx.cur_elmt++) */ } /* end for (blkndx = 0; blkndx < nblocks; blkndx++) */ @@ -1434,7 +1459,7 @@ done: } /* end h5str_print_region_data_blocks */ int -h5str_dump_region_blocks_data(JNIEnv *env, h5str_t *str, hid_t region, hid_t region_id) +h5str_dump_region_blocks(JNIEnv *env, h5str_t *str, hid_t region_space, hid_t region_id, int expand_data) { hssize_t nblocks; hsize_t alloc_size; @@ -1443,32 +1468,34 @@ h5str_dump_region_blocks_data(JNIEnv *env, h5str_t *str, hid_t region, hid_t reg hid_t type_id = H5I_INVALID_HID; int ndims = -1; int ret_value = FAIL; + int i; + char tmp_str[256]; /* * This function fails if the region does not have blocks. */ H5E_BEGIN_TRY { - nblocks = H5Sget_select_hyper_nblocks(region); + nblocks = H5Sget_select_hyper_nblocks(region_space); } H5E_END_TRY; - if (nblocks < 0) - H5_LIBRARY_ERROR(ENVONLY); - - if ((ndims = H5Sget_simple_extent_ndims(region)) < 0) + if (nblocks <= 0) { + ret_value = SUCCEED; + goto done; + } + if ((ndims = H5Sget_simple_extent_ndims(region_space)) < 0) H5_LIBRARY_ERROR(ENVONLY); /* Print block information */ alloc_size = (hsize_t)nblocks * (hsize_t)ndims * 2 * (hsize_t)sizeof(ptdata[0]); - if (alloc_size == (hsize_t)((size_t)alloc_size)) { - if (NULL == (ptdata = (hsize_t *)HDmalloc((size_t)alloc_size))) - H5_OUT_OF_MEMORY_ERROR(ENVONLY, - "h5str_dump_region_blocks_data: failed to allocate region block buffer"); + if (NULL == (ptdata = (hsize_t *)HDmalloc((size_t)alloc_size))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_dump_region_blocks: failed to allocate region block buffer"); - if (H5Sget_select_hyper_blocklist(region, (hsize_t)0, (hsize_t)nblocks, ptdata) < 0) - H5_LIBRARY_ERROR(ENVONLY); + if (H5Sget_select_hyper_blocklist(region_space, (hsize_t)0, (hsize_t)nblocks, ptdata) < 0) + H5_LIBRARY_ERROR(ENVONLY); + if (expand_data) { if ((dtype = H5Dget_type(region_id)) < 0) H5_LIBRARY_ERROR(ENVONLY); @@ -1477,69 +1504,19 @@ h5str_dump_region_blocks_data(JNIEnv *env, h5str_t *str, hid_t region, hid_t reg if (h5str_print_region_data_blocks(ENVONLY, region_id, str, ndims, type_id, nblocks, ptdata) < 0) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - } /* if (alloc_size == (hsize_t)((size_t)alloc_size)) */ - - ret_value = SUCCEED; - -done: - if (type_id >= 0) - H5Tclose(type_id); - if (dtype >= 0) - H5Tclose(dtype); - if (ptdata) - HDfree(ptdata); - - return ret_value; -} /* end h5str_dump_region_blocks_data */ - -#ifndef SKIP_UNUSED_DUMP_ROUTINES -static int -h5str_dump_region_blocks(JNIEnv *env, h5str_t *str, hid_t region, hid_t region_id) -{ - hssize_t nblocks; - hsize_t alloc_size; - hsize_t *ptdata = NULL; - char tmp_str[256]; - int ndims = -1; - int ret_value = FAIL; - - UNUSED(region_id); - - /* - * This function fails if the region does not have blocks. - */ - H5E_BEGIN_TRY - { - nblocks = H5Sget_select_hyper_nblocks(region); } - H5E_END_TRY; - - if (nblocks < 0) - H5_LIBRARY_ERROR(ENVONLY); - - if ((ndims = H5Sget_simple_extent_ndims(region)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - - /* Print block information */ - alloc_size = (hsize_t)nblocks * (hsize_t)ndims * 2 * (hsize_t)sizeof(ptdata[0]); - if (alloc_size == (hsize_t)((size_t)alloc_size)) { - int i; - - if (NULL == (ptdata = (hsize_t *)HDmalloc((size_t)alloc_size))) - H5_OUT_OF_MEMORY_ERROR(ENVONLY, - "h5str_dump_region_blocks: failed to allocate region block buffer"); - - if (H5Sget_select_hyper_blocklist(region, (hsize_t)0, (hsize_t)nblocks, ptdata) < 0) - H5_LIBRARY_ERROR(ENVONLY); + else { + if (!h5str_append(str, " REGION_TYPE BLOCK")) + H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); if (!h5str_append(str, " {")) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); for (i = 0; i < nblocks; i++) { int j; if (!h5str_append(str, " ")) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); /* Start coordinates and opposite corner */ for (j = 0; j < ndims; j++) { @@ -1549,7 +1526,7 @@ h5str_dump_region_blocks(JNIEnv *env, h5str_t *str, hid_t region, hid_t region_i H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_region_blocks: HDsprintf failure"); if (!h5str_append(str, tmp_str)) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); } for (j = 0; j < ndims; j++) { @@ -1560,28 +1537,30 @@ h5str_dump_region_blocks(JNIEnv *env, h5str_t *str, hid_t region, hid_t region_i H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_region_blocks: HDsprintf failure"); if (!h5str_append(str, tmp_str)) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); } if (!h5str_append(str, ") ")) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); tmp_str[0] = '\0'; } if (!h5str_append(str, " }")) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - } /* if (alloc_size == (hsize_t)((size_t)alloc_size)) */ - + H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); + } ret_value = SUCCEED; done: + if (type_id >= 0) + H5Tclose(type_id); + if (dtype >= 0) + H5Tclose(dtype); if (ptdata) HDfree(ptdata); return ret_value; } /* end h5str_dump_region_blocks */ -#endif /*------------------------------------------------------------------------- * Purpose: Print the data values from a dataset referenced by region points. @@ -1634,12 +1613,12 @@ h5str_print_region_data_points(JNIEnv *env, hid_t region_space, hid_t region_id, if (H5Sget_simple_extent_dims(mem_space, total_size, NULL) < 0) H5_LIBRARY_ERROR(ENVONLY); - if (!h5str_sprintf(ENVONLY, str, region_id, type_id, ((char *)region_buf + jndx * type_size), 0, 1)) + if (!h5str_sprintf(ENVONLY, str, region_id, type_id, ((char *)region_buf + jndx * type_size), 1)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); if (jndx + 1 < (size_t)npoints) if (!h5str_append(str, ", ")) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); } /* end for (jndx = 0; jndx < npoints; jndx++, elmtno++) */ ret_value = SUCCEED; @@ -1656,146 +1635,96 @@ done: } /* end h5str_print_region_data_points */ int -h5str_dump_region_points_data(JNIEnv *env, h5str_t *str, hid_t region, hid_t region_id) +h5str_dump_region_points(JNIEnv *env, h5str_t *str, hid_t region_space, hid_t region_id, int expand_data) { - hssize_t npoints; hsize_t alloc_size; + hssize_t npoints = -1; hsize_t *ptdata = NULL; hid_t dtype = H5I_INVALID_HID; hid_t type_id = H5I_INVALID_HID; int ndims = -1; int ret_value = FAIL; + int i; + char tmp_str[256]; /* * This function fails if the region does not have points. */ H5E_BEGIN_TRY { - npoints = H5Sget_select_elem_npoints(region); + npoints = H5Sget_select_elem_npoints(region_space); } H5E_END_TRY; - if (npoints < 0) - H5_LIBRARY_ERROR(ENVONLY); - - if ((ndims = H5Sget_simple_extent_ndims(region)) < 0) + if (npoints <= 0) { + ret_value = SUCCEED; + goto done; + } + if ((ndims = H5Sget_simple_extent_ndims(region_space)) < 0) H5_LIBRARY_ERROR(ENVONLY); /* Print point information */ - if (npoints > 0) { - alloc_size = (hsize_t)npoints * (hsize_t)ndims * (hsize_t)sizeof(ptdata[0]); - if (alloc_size == (hsize_t)((size_t)alloc_size)) { - if (NULL == (ptdata = (hsize_t *)HDmalloc((size_t)alloc_size))) - H5_OUT_OF_MEMORY_ERROR( - ENVONLY, "h5str_dump_region_points_data: failed to allocate region point data buffer"); - - if (H5Sget_select_elem_pointlist(region, (hsize_t)0, (hsize_t)npoints, ptdata) < 0) - H5_LIBRARY_ERROR(ENVONLY); - - if ((dtype = H5Dget_type(region_id)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - - if ((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - - if (h5str_print_region_data_points(ENVONLY, region, region_id, str, ndims, type_id, npoints, - ptdata) < 0) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - } - } - - ret_value = SUCCEED; - -done: - if (type_id >= 0) - H5Tclose(type_id); - if (dtype >= 0) - H5Tclose(dtype); - if (ptdata) - HDfree(ptdata); - - return ret_value; -} /* end h5str_dump_region_points_data */ - -#ifndef SKIP_UNUSED_DUMP_ROUTINES -static int -h5str_dump_region_points(JNIEnv *env, h5str_t *str, hid_t region, hid_t region_id) -{ - hssize_t npoints; - hsize_t alloc_size; - hsize_t *ptdata = NULL; - char tmp_str[256]; - int ndims = -1; - int ret_value = FAIL; - - UNUSED(region_id); - - /* - * This function fails if the region does not have points. - */ - H5E_BEGIN_TRY - { - npoints = H5Sget_select_elem_npoints(region); - } - H5E_END_TRY; - - if (npoints < 0) - H5_LIBRARY_ERROR(ENVONLY); + alloc_size = (hsize_t)npoints * (hsize_t)ndims * (hsize_t)sizeof(ptdata[0]); + if (NULL == (ptdata = (hsize_t *)HDmalloc((size_t)alloc_size))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, + "h5str_dump_region_points: failed to allocate region point data buffer"); - if ((ndims = H5Sget_simple_extent_ndims(region)) < 0) + if (H5Sget_select_elem_pointlist(region_space, (hsize_t)0, (hsize_t)npoints, ptdata) < 0) H5_LIBRARY_ERROR(ENVONLY); - /* Print point information */ - if (npoints > 0) { - int i; - - alloc_size = (hsize_t)npoints * (hsize_t)ndims * (hsize_t)sizeof(ptdata[0]); - if (alloc_size == (hsize_t)((size_t)alloc_size)) { - if (NULL == (ptdata = (hsize_t *)HDmalloc((size_t)alloc_size))) - H5_OUT_OF_MEMORY_ERROR(ENVONLY, - "h5str_dump_region_points: failed to allocate region point buffer"); + if (expand_data) { + if ((dtype = H5Dget_type(region_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); - if (H5Sget_select_elem_pointlist(region, (hsize_t)0, (hsize_t)npoints, ptdata) < 0) - H5_LIBRARY_ERROR(ENVONLY); + if ((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) < 0) + H5_LIBRARY_ERROR(ENVONLY); - if (!h5str_append(str, " {")) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + if (h5str_print_region_data_points(ENVONLY, region_space, region_id, str, ndims, type_id, npoints, + ptdata) < 0) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + } + else { + if (!h5str_append(str, " REGION_TYPE POINT")) + H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); - for (i = 0; i < npoints; i++) { - int j; + if (!h5str_append(str, " {")) + H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); - if (!h5str_append(str, " ")) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + for (i = 0; i < npoints; i++) { + int j; - for (j = 0; j < ndims; j++) { - tmp_str[0] = '\0'; + if (!h5str_append(str, " ")) + H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); - if (HDsprintf(tmp_str, "%s%lu", j ? "," : "(", (unsigned long)(ptdata[i * ndims + j])) < - 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_region_points: HDsprintf failure"); + for (j = 0; j < ndims; j++) { + tmp_str[0] = '\0'; - if (!h5str_append(str, tmp_str)) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - } /* end for (j = 0; j < ndims; j++) */ + if (HDsprintf(tmp_str, "%s%lu", j ? "," : "(", (unsigned long)(ptdata[i * ndims + j])) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_region_points: HDsprintf failure"); - if (!h5str_append(str, ") ")) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - } /* end for (i = 0; i < npoints; i++) */ + if (!h5str_append(str, tmp_str)) + H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); + } /* end for (j = 0; j < ndims; j++) */ - if (!h5str_append(str, " }")) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - } /* end if (alloc_size == (hsize_t)((size_t) alloc_size)) */ - } /* end if (npoints > 0) */ + if (!h5str_append(str, ") ")) + H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); + } /* end for (i = 0; i < npoints; i++) */ + if (!h5str_append(str, " }")) + H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); + } ret_value = SUCCEED; done: + if (type_id >= 0) + H5Tclose(type_id); + if (dtype >= 0) + H5Tclose(dtype); if (ptdata) HDfree(ptdata); return ret_value; } /* end h5str_dump_region_points */ -#endif static int h5str_is_zero(const void *_mem, size_t size) @@ -2312,47 +2241,31 @@ h5str_render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hs } case H5T_REFERENCE: { - if (H5Tequal(tid, H5T_STD_REF)) { - hid_t region_id = H5I_INVALID_HID; - hid_t region_space = H5I_INVALID_HID; - H5S_sel_type region_type; - - /* Region data */ - for (block_index = 0; block_index < block_nelmts; block_index++) { - mem = ((unsigned char *)_mem) + block_index * size; - if ((region_id = H5Ropen_object((const H5R_ref_t *)mem, H5P_DEFAULT, H5P_DEFAULT)) < 0) - continue; - else { - if ((region_space = - H5Ropen_region((const H5R_ref_t *)mem, H5P_DEFAULT, H5P_DEFAULT)) >= 0) { - if (!h5str_is_zero(mem, H5Tget_size(H5T_STD_REF))) { - region_type = H5Sget_select_type(region_space); - if (region_type == H5S_SEL_POINTS) - ret_value = render_bin_output_region_points(stream, region_space, - region_id, container); - else - ret_value = render_bin_output_region_blocks(stream, region_space, - region_id, container); - } - H5Sclose(region_space); - } /* end if (region_space >= 0) */ - H5Dclose(region_id); - } + hid_t region_id = H5I_INVALID_HID; + hid_t region_space = H5I_INVALID_HID; + H5S_sel_type region_type; - if ((region_type = H5Sget_select_type(region_space)) < 0) { - H5Sclose(region_space); - H5Dclose(region_id); - continue; + /* Region data */ + for (block_index = 0; block_index < block_nelmts; block_index++) { + mem = ((unsigned char *)_mem) + block_index * size; + if ((region_id = H5Ropen_object((H5R_ref_t *)mem, H5P_DEFAULT, H5P_DEFAULT)) < 0) + continue; + if ((region_space = H5Ropen_region((H5R_ref_t *)mem, H5P_DEFAULT, H5P_DEFAULT)) >= 0) { + if (!h5str_is_zero(mem, H5Tget_size(H5T_STD_REF))) { + region_type = H5Sget_select_type(region_space); + if (region_type == H5S_SEL_POINTS) + ret_value = + render_bin_output_region_points(stream, region_space, region_id, container); + else if (region_type == H5S_SEL_HYPERSLABS) + ret_value = + render_bin_output_region_blocks(stream, region_space, region_id, container); } - if (ret_value < 0) - break; - } - } - else if (H5Tequal(tid, H5T_STD_REF_DSETREG)) { - ; - } - else if (H5Tequal(tid, H5T_STD_REF_OBJ)) { - ; + H5Sclose(region_space); + } /* end if (region_space >= 0) */ + H5Dclose(region_id); + + if (ret_value < 0) + break; } break; @@ -2723,6 +2636,109 @@ done: return ret_value; } /* end render_bin_output_region_points */ +/*------------------------------------------------------------------------- + * Purpose: Print some values from an attribute referenced by object reference. + * + * Parameters Description: + * FILE *buffer is the string into which to render + *------------------------------------------------------------------------- + */ +static int +h5str_dump_region_attribute(JNIEnv *env, h5str_t *str, hid_t region_id) +{ + int ret_value = SUCCEED; + hid_t atype = H5I_INVALID_HID; + hid_t type_id = H5I_INVALID_HID; + hid_t region_space = H5I_INVALID_HID; + hsize_t total_size[H5S_MAX_RANK]; /* total size of dataset*/ + size_t i; /* counter */ + size_t size; /* datum size */ + int sndims; /* rank of dataspace */ + hsize_t p_nelmts; /* total selected elmts */ + hsize_t alloc_size; + + unsigned char *buf = NULL; /* buffer for raw data */ + + /* VL data special information */ + unsigned int vl_data = 0; /* contains VL datatypes */ + + if ((region_space = H5Aget_space(region_id)) < 0) { + ret_value = FAIL; + goto done; + } + + if ((sndims = H5Sget_simple_extent_ndims(region_space)) < 0) { + ret_value = FAIL; + goto done; + } + + /* Assume entire data space to be read */ + H5Sget_simple_extent_dims(region_space, total_size, NULL); + p_nelmts = 1; + + for (i = 0; i < sndims; i++) + p_nelmts *= total_size[i]; + + if ((atype = H5Aget_type(region_id)) < 0) { + ret_value = FAIL; + goto done; + } + if ((type_id = H5Tget_native_type(atype, H5T_DIR_DEFAULT)) < 0) { + ret_value = FAIL; + goto done; + } + + /* Check if we have VL data in the dataset's datatype */ + if (h5str_detect_vlen(type_id) == TRUE) + vl_data = TRUE; + + if (!(size = H5Tget_size(type_id))) { + ret_value = FAIL; + goto done; + } + + alloc_size = p_nelmts * size; + HDassert(alloc_size == (hsize_t)((size_t)alloc_size)); /*check for overflow*/ + if (NULL != (buf = (unsigned char *)HDmalloc((size_t)alloc_size))) { + /* Read the data */ + if (H5Aread(region_id, type_id, buf) >= 0) { + + for (i = 0; i < p_nelmts; i++) { + size_t bytes_in = 0; /* # of bytes to write */ + void * memref = buf + i * size; + + if (!(bytes_in = h5str_sprintf(ENVONLY, str, region_id, type_id, memref, 1))) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + + if ((i < p_nelmts - 1) && (bytes_in > 0)) { + if (!h5str_append(str, ", ")) + H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); + } + } + + /* Reclaim any VL memory, if necessary */ + if (vl_data) { + if (H5Treclaim(type_id, region_space, H5P_DEFAULT, buf) < 0) + H5_LIBRARY_ERROR(ENVONLY); + } + } + else + H5_LIBRARY_ERROR(ENVONLY); + } + +done: + if (buf) + HDfree(buf); + if (region_space >= 0) + H5Sclose(region_space); + if (type_id >= 0) + H5Tclose(type_id); + if (atype >= 0) + H5Tclose(type_id); + + return ret_value; +} + int h5str_dump_simple_dset(JNIEnv *env, FILE *stream, hid_t dset, int binary_order) { @@ -2739,11 +2755,11 @@ h5str_dump_simple_dset(JNIEnv *env, FILE *stream, hid_t dset, int binary_order) size_t p_type_nbytes; /* size of memory type */ /* Stripmine info */ - unsigned char *sm_buf = NULL; /* buffer for raw data */ - hsize_t sm_size[H5S_MAX_RANK]; /* stripmine size */ - hsize_t sm_nbytes; /* bytes per stripmine */ - hsize_t sm_nelmts; /* elements per stripmine */ - hid_t sm_space = H5I_INVALID_HID; /* stripmine data space */ + void * sm_buf = NULL; /* buffer for raw data */ + hsize_t sm_size[H5S_MAX_RANK]; /* stripmine size */ + hsize_t sm_nbytes; /* bytes per stripmine */ + hsize_t sm_nelmts; /* elements per stripmine */ + hid_t sm_space = H5I_INVALID_HID; /* stripmine data space */ /* Hyperslab info */ hsize_t hs_offset[H5S_MAX_RANK]; /* starting offset */ @@ -2763,142 +2779,168 @@ h5str_dump_simple_dset(JNIEnv *env, FILE *stream, hid_t dset, int binary_order) if ((f_type = H5Dget_type(dset)) < 0) H5_LIBRARY_ERROR(ENVONLY); - switch (binary_order) { - case 1: { - if ((p_type = h5str_get_native_type(f_type)) < 0) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + if ((f_space = H5Dget_space(dset)) < 0) + H5_LIBRARY_ERROR(ENVONLY); - break; - } + if ((ndims = H5Sget_simple_extent_ndims(f_space)) < 0) + H5_LIBRARY_ERROR(ENVONLY); - case 2: { - if ((p_type = h5str_get_little_endian_type(f_type)) < 0) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + if (H5Sget_simple_extent_dims(f_space, total_size, NULL) < 0) + H5_LIBRARY_ERROR(ENVONLY); - break; - } + if (H5Tequal(f_type, H5T_STD_REF_DSETREG)) { + p_nelmts = H5Sget_simple_extent_npoints(f_space); + if (NULL == + (sm_buf = (H5R_ref_t *)HDcalloc(MAX(sizeof(unsigned), sizeof(H5R_ref_t)), (size_t)p_nelmts))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_dump_simple_mem: failed to allocate sm_buf"); - case 3: { - if ((p_type = h5str_get_big_endian_type(f_type)) < 0) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + /* Read the data */ + if (H5Dread(dset, H5T_STD_REF, H5S_ALL, H5S_ALL, H5P_DEFAULT, sm_buf) < 0) + H5_LIBRARY_ERROR(ENVONLY); - break; + if (binary_order == 99) { + if (h5str_dump_simple_data(ENVONLY, stream, dset, H5T_STD_REF, sm_buf, p_nelmts) < 0) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); } - - default: { - if ((p_type = H5Tcopy(f_type)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - - break; + else { + if (h5str_render_bin_output(stream, dset, H5T_STD_REF, sm_buf, p_nelmts) < 0) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); } } + else { + switch (binary_order) { + case 1: { + if ((p_type = h5str_get_native_type(f_type)) < 0) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - if ((f_space = H5Dget_space(dset)) < 0) - H5_LIBRARY_ERROR(ENVONLY); + break; + } - if ((ndims = H5Sget_simple_extent_ndims(f_space)) < 0) - H5_LIBRARY_ERROR(ENVONLY); + case 2: { + if ((p_type = h5str_get_little_endian_type(f_type)) < 0) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - if ((size_t)ndims <= (sizeof(sm_size) / sizeof(sm_size[0]))) { - if (H5Sget_simple_extent_dims(f_space, total_size, NULL) < 0) - H5_LIBRARY_ERROR(ENVONLY); + break; + } - /* Calculate the number of elements we're going to print */ - p_nelmts = 1; + case 3: { + if ((p_type = h5str_get_big_endian_type(f_type)) < 0) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - if (ndims > 0) { - for (i = 0; i < (size_t)ndims; i++) - p_nelmts *= total_size[i]; - } /* end if */ + break; + } + + default: { + if ((p_type = H5Tcopy(f_type)) < 0) + H5_LIBRARY_ERROR(ENVONLY); - if (p_nelmts > 0) { - /* Check if we have VL data in the dataset's datatype */ - if (h5str_detect_vlen(p_type) != 0) - vl_data = 1; + break; + } + } - /* - * Determine the strip mine size and allocate a buffer. The strip mine is - * a hyperslab whose size is manageable. - */ - if (!(sm_nbytes = p_type_nbytes = H5Tget_size(p_type))) + if ((size_t)ndims <= (sizeof(sm_size) / sizeof(sm_size[0]))) { + if (H5Sget_simple_extent_dims(f_space, total_size, NULL) < 0) H5_LIBRARY_ERROR(ENVONLY); + /* Calculate the number of elements we're going to print */ + p_nelmts = 1; + if (ndims > 0) { - for (i = (size_t)ndims; i > 0; --i) { - hsize_t size = H5TOOLS_BUFSIZE / sm_nbytes; - if (size == 0) /* datum size > H5TOOLS_BUFSIZE */ - size = 1; - sm_size[i - 1] = (((total_size[i - 1]) < (size)) ? (total_size[i - 1]) : (size)); - sm_nbytes *= sm_size[i - 1]; + for (i = 0; i < (size_t)ndims; i++) + p_nelmts *= total_size[i]; + } /* end if */ + + if (p_nelmts > 0) { + /* Check if we have VL data in the dataset's datatype */ + if (h5str_detect_vlen(p_type) != 0) + vl_data = 1; + + /* + * Determine the strip mine size and allocate a buffer. The strip mine is + * a hyperslab whose size is manageable. + */ + if (!(sm_nbytes = p_type_nbytes = H5Tget_size(p_type))) + H5_LIBRARY_ERROR(ENVONLY); + + if (ndims > 0) { + for (i = (size_t)ndims; i > 0; --i) { + hsize_t size = H5TOOLS_BUFSIZE / sm_nbytes; + if (size == 0) /* datum size > H5TOOLS_BUFSIZE */ + size = 1; + sm_size[i - 1] = (((total_size[i - 1]) < (size)) ? (total_size[i - 1]) : (size)); + sm_nbytes *= sm_size[i - 1]; + } } - } - if (sm_nbytes > 0) { - if (NULL == (sm_buf = (unsigned char *)HDmalloc((size_t)sm_nbytes))) - H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_dump_simple_dset: failed to allocate sm_buf"); + if (sm_nbytes > 0) { + if (NULL == (sm_buf = (unsigned char *)HDmalloc((size_t)sm_nbytes))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_dump_simple_dset: failed to allocate sm_buf"); - sm_nelmts = sm_nbytes / p_type_nbytes; + sm_nelmts = sm_nbytes / p_type_nbytes; - if ((sm_space = H5Screate_simple(1, &sm_nelmts, NULL)) < 0) - H5_LIBRARY_ERROR(ENVONLY); + if ((sm_space = H5Screate_simple(1, &sm_nelmts, NULL)) < 0) + H5_LIBRARY_ERROR(ENVONLY); - /* The stripmine loop */ - HDmemset(hs_offset, 0, sizeof hs_offset); - HDmemset(zero, 0, sizeof zero); - - for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_nelmts) { - /* Calculate the hyperslab size */ - if (ndims > 0) { - for (i = 0, hs_nelmts = 1; i < (size_t)ndims; i++) { - hs_size[i] = (((total_size[i] - hs_offset[i]) < (sm_size[i])) - ? (total_size[i] - hs_offset[i]) - : (sm_size[i])); - hs_nelmts *= hs_size[i]; - } + /* The stripmine loop */ + HDmemset(hs_offset, 0, sizeof hs_offset); + HDmemset(zero, 0, sizeof zero); + + for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_nelmts) { + /* Calculate the hyperslab size */ + if (ndims > 0) { + for (i = 0, hs_nelmts = 1; i < (size_t)ndims; i++) { + hs_size[i] = (((total_size[i] - hs_offset[i]) < (sm_size[i])) + ? (total_size[i] - hs_offset[i]) + : (sm_size[i])); + hs_nelmts *= hs_size[i]; + } - if (H5Sselect_hyperslab(f_space, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL) < 0) - H5_LIBRARY_ERROR(ENVONLY); + if (H5Sselect_hyperslab(f_space, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL) < + 0) + H5_LIBRARY_ERROR(ENVONLY); - if (H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL, &hs_nelmts, NULL) < 0) - H5_LIBRARY_ERROR(ENVONLY); - } - else { - if (H5Sselect_all(f_space) < 0) - H5_LIBRARY_ERROR(ENVONLY); + if (H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL, &hs_nelmts, NULL) < + 0) + H5_LIBRARY_ERROR(ENVONLY); + } + else { + if (H5Sselect_all(f_space) < 0) + H5_LIBRARY_ERROR(ENVONLY); - if (H5Sselect_all(sm_space) < 0) - H5_LIBRARY_ERROR(ENVONLY); + if (H5Sselect_all(sm_space) < 0) + H5_LIBRARY_ERROR(ENVONLY); - hs_nelmts = 1; - } + hs_nelmts = 1; + } - /* Read the data */ - if (H5Dread(dset, p_type, sm_space, f_space, H5P_DEFAULT, sm_buf) < 0) - H5_LIBRARY_ERROR(ENVONLY); + /* Read the data */ + if (H5Dread(dset, p_type, sm_space, f_space, H5P_DEFAULT, sm_buf) < 0) + H5_LIBRARY_ERROR(ENVONLY); - if (binary_order == 99) { - if (h5tools_dump_simple_data(ENVONLY, stream, dset, p_type, sm_buf, hs_nelmts) < 0) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - } - else { - if (h5str_render_bin_output(stream, dset, p_type, sm_buf, hs_nelmts) < 0) - CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - } + if (binary_order == 99) { + if (h5str_dump_simple_data(ENVONLY, stream, dset, p_type, sm_buf, hs_nelmts) < 0) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + } + else { + if (h5str_render_bin_output(stream, dset, p_type, sm_buf, hs_nelmts) < 0) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + } - /* Reclaim any VL memory, if necessary */ - if (vl_data) { - if (H5Treclaim(p_type, sm_space, H5P_DEFAULT, sm_buf) < 0) - H5_LIBRARY_ERROR(ENVONLY); - } + /* Reclaim any VL memory, if necessary */ + if (vl_data) { + if (H5Treclaim(p_type, sm_space, H5P_DEFAULT, sm_buf) < 0) + H5_LIBRARY_ERROR(ENVONLY); + } - /* Calculate the next hyperslab offset */ - for (i = (size_t)ndims, carry = 1; i > 0 && carry; --i) { - hs_offset[i - 1] += hs_size[i - 1]; + /* Calculate the next hyperslab offset */ + for (i = (size_t)ndims, carry = 1; i > 0 && carry; --i) { + hs_offset[i - 1] += hs_size[i - 1]; - if (hs_offset[i - 1] == total_size[i - 1]) - hs_offset[i - 1] = 0; - else - carry = 0; + if (hs_offset[i - 1] == total_size[i - 1]) + hs_offset[i - 1] = 0; + else + carry = 0; + } } } } @@ -2922,6 +2964,148 @@ done: return ret_value; } /* end h5str_dump_simple_dset */ +int +h5str_dump_simple_mem(JNIEnv *env, FILE *stream, hid_t attr_id, int binary_order) +{ + hid_t f_space = H5I_INVALID_HID; /* file data space */ + hsize_t alloc_size; + int ndims; /* rank of dataspace */ + unsigned i; /* counters */ + hsize_t total_size[H5S_MAX_RANK]; /* total size of dataset*/ + hsize_t p_nelmts; /* total selected elmts */ + + void * sm_buf = NULL; /* buffer for raw data */ + hsize_t sm_size[H5S_MAX_RANK]; /* stripmine size */ + + int ret_value = 0; + + /* VL data special information */ + unsigned int vl_data = 0; /* contains VL datatypes */ + hid_t p_type = H5I_INVALID_HID; + hid_t f_type = H5I_INVALID_HID; + + if (attr_id < 0) + H5_BAD_ARGUMENT_ERROR(ENVONLY, "h5str_dump_simple_mem: attr ID < 0"); + + if ((f_type = H5Aget_type(attr_id)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + if (H5I_INVALID_HID == (f_space = H5Aget_space(attr_id))) + H5_LIBRARY_ERROR(ENVONLY); + + if ((ndims = H5Sget_simple_extent_ndims(f_space)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + if (H5Sget_simple_extent_dims(f_space, total_size, NULL) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + if (H5Tequal(f_type, H5T_STD_REF_DSETREG)) { + p_nelmts = H5Sget_simple_extent_npoints(f_space); + if (NULL == + (sm_buf = (H5R_ref_t *)HDcalloc(MAX(sizeof(unsigned), sizeof(H5R_ref_t)), (size_t)p_nelmts))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_dump_simple_mem: failed to allocate sm_buf"); + + /* Read the data */ + if (H5Aread(attr_id, H5T_STD_REF, sm_buf) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + if (binary_order == 99) { + if (h5str_dump_simple_data(ENVONLY, stream, attr_id, H5T_STD_REF, sm_buf, p_nelmts) < 0) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + } + else { + if (h5str_render_bin_output(stream, attr_id, H5T_STD_REF, sm_buf, p_nelmts) < 0) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + } + } + else { + switch (binary_order) { + case 1: { + if ((p_type = h5str_get_native_type(f_type)) < 0) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + + break; + } + + case 2: { + if ((p_type = h5str_get_little_endian_type(f_type)) < 0) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + + break; + } + + case 3: { + if ((p_type = h5str_get_big_endian_type(f_type)) < 0) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + + break; + } + + default: { + if ((p_type = H5Tcopy(f_type)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + break; + } + } + + if ((size_t)ndims <= (sizeof(sm_size) / sizeof(sm_size[0]))) { + if (H5Sget_simple_extent_dims(f_space, total_size, NULL) < 0) + H5_LIBRARY_ERROR(ENVONLY); + /* Calculate the number of elements we're going to print */ + p_nelmts = 1; + + if (ndims > 0) { + for (i = 0; i < (size_t)ndims; i++) + p_nelmts *= total_size[i]; + } /* end if */ + + if (p_nelmts > 0) { + /* Check if we have VL data in the dataset's datatype */ + if (h5str_detect_vlen(p_type) != 0) + vl_data = 1; + + alloc_size = p_nelmts * H5Tget_size(p_type); + if (NULL == (sm_buf = (unsigned char *)HDmalloc((size_t)alloc_size))) + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_dump_simple_mem: failed to allocate sm_buf"); + + /* Read the data */ + if (H5Aread(attr_id, p_type, sm_buf) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + if (binary_order == 99) { + if (h5str_dump_simple_data(ENVONLY, stream, attr_id, p_type, sm_buf, p_nelmts) < 0) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + } + else { + if (h5str_render_bin_output(stream, attr_id, p_type, sm_buf, p_nelmts) < 0) + CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); + } + + /* Reclaim any VL memory, if necessary */ + if (vl_data) { + if (H5Treclaim(p_type, f_space, H5P_DEFAULT, sm_buf) < 0) + H5_LIBRARY_ERROR(ENVONLY); + } + } + } + } + + ret_value = SUCCEED; + +done: + if (sm_buf) + HDfree(sm_buf); + if (f_space >= 0) + H5Sclose(f_space); + if (p_type >= 0) + H5Tclose(p_type); + if (f_type >= 0) + H5Tclose(f_type); + + return ret_value; +} + htri_t H5Tdetect_variable_str(hid_t tid) { @@ -2948,7 +3132,7 @@ H5Tdetect_variable_str(hid_t tid) } /* end H5Tdetect_variable_str */ static int -h5tools_dump_simple_data(JNIEnv *env, FILE *stream, hid_t container, hid_t type, void *_mem, hsize_t nelmts) +h5str_dump_simple_data(JNIEnv *env, FILE *stream, hid_t container, hid_t type, void *_mem, hsize_t nelmts) { unsigned char *mem = (unsigned char *)_mem; h5str_t buffer; /* string into which to render */ @@ -2968,38 +3152,37 @@ h5tools_dump_simple_data(JNIEnv *env, FILE *stream, hid_t container, hid_t type, h5str_new(&buffer, 32 * size); if (!buffer.s) - H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5tools_dump_simple_data: failed to allocate buffer"); + H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_dump_simple_data: failed to allocate buffer"); - if (!(bytes_in = h5str_sprintf(ENVONLY, &buffer, container, type, memref, 0, 1))) + if (!(bytes_in = h5str_sprintf(ENVONLY, &buffer, container, type, memref, 1))) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); - if (i > 0) { + if ((i > 0) && (bytes_in > 0)) { if (HDfprintf(stream, ", ") < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5tools_dump_simple_data: HDfprintf failure"); + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_simple_data: HDfprintf failure"); if (line_count >= H5TOOLS_TEXT_BLOCK) { line_count = 0; if (HDfprintf(stream, "\n") < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5tools_dump_simple_data: HDfprintf failure"); + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_simple_data: HDfprintf failure"); } } - if (HDfprintf(stream, "%s", buffer.s) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5tools_dump_simple_data: HDfprintf failure"); + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_simple_data: HDfprintf failure"); h5str_free(&buffer); } /* end for (i = 0; i < nelmts... */ if (HDfprintf(stream, "\n") < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5tools_dump_simple_data: HDfprintf failure"); + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_simple_data: HDfprintf failure"); done: if (buffer.s) h5str_free(&buffer); return ret_value; -} /* end h5tools_dump_simple_data */ +} /* end h5str_dump_simple_data */ /* * Utility Java APIs @@ -3053,7 +3236,7 @@ Java_hdf_hdf5lib_H5_H5AreadComplex(JNIEnv *env, jclass clss, jlong attr_id, jlon for (i = 0; i < (size_t)n; i++) { h5str.s[0] = '\0'; - if (!h5str_sprintf(ENVONLY, &h5str, attr_id, mem_type_id, readBuf + (i * size), 0, 0)) + if (!h5str_sprintf(ENVONLY, &h5str, attr_id, mem_type_id, readBuf + (i * size), 0)) CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE); if (NULL == (jstr = ENVPTR->NewStringUTF(ENVONLY, h5str.s))) @@ -3554,18 +3737,16 @@ done: /* * Class: hdf_hdf5lib_H5 * Method: H5export_dataset - * Signature: (Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;I)V + * Signature: (Ljava/lang/String;JLjava/lang/String;I)V */ JNIEXPORT void JNICALL -Java_hdf_hdf5lib_H5_H5export_1dataset(JNIEnv *env, jclass clss, jstring file_export_name, jstring file_name, +Java_hdf_hdf5lib_H5_H5export_1dataset(JNIEnv *env, jclass clss, jstring file_export_name, jlong file_id, jstring object_path, jint binary_order) { const char *file_export = NULL; const char *object_name = NULL; - const char *fileName = NULL; jboolean isCopy; herr_t ret_val = FAIL; - hid_t file_id = H5I_INVALID_HID; hid_t dataset_id = H5I_INVALID_HID; FILE * stream = NULL; @@ -3574,17 +3755,9 @@ Java_hdf_hdf5lib_H5_H5export_1dataset(JNIEnv *env, jclass clss, jstring file_exp if (NULL == file_export_name) H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5export_dataset: file_export_name is NULL"); - if (NULL == file_name) - H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5export_dataset: file_name is NULL"); - if (NULL == object_path) H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5export_dataset: object_path is NULL"); - PIN_JAVA_STRING(ENVONLY, file_name, fileName, NULL, "H5export_dataset: file name not pinned"); - - if ((file_id = H5Fopen(fileName, (unsigned)H5F_ACC_RDWR, (hid_t)H5P_DEFAULT)) < 0) - H5_LIBRARY_ERROR(ENVONLY); - PIN_JAVA_STRING(ENVONLY, object_path, object_name, &isCopy, "H5export_dataset: object_path not pinned"); if ((dataset_id = H5Dopen2(file_id, object_name, H5P_DEFAULT)) < 0) @@ -3597,7 +3770,7 @@ Java_hdf_hdf5lib_H5_H5export_1dataset(JNIEnv *env, jclass clss, jstring file_exp H5_JNI_FATAL_ERROR(ENVONLY, "HDfopen failed"); if ((ret_val = h5str_dump_simple_dset(ENVONLY, stream, dataset_id, binary_order)) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_simple_dset failed"); + H5_ASSERTION_ERROR(ENVONLY, "h5str_dump_simple_dset failed"); if (stream) { HDfclose(stream); @@ -3611,14 +3784,65 @@ done: UNPIN_JAVA_STRING(ENVONLY, file_export_name, file_export); if (object_name) UNPIN_JAVA_STRING(ENVONLY, object_path, object_name); - if (fileName) - UNPIN_JAVA_STRING(ENVONLY, file_name, fileName); if (dataset_id >= 0) H5Dclose(dataset_id); - if (file_id >= 0) - H5Fclose(file_id); } /* end Java_hdf_hdf5lib_H5_H5export_1dataset */ +/* + * Class: hdf_hdf5lib_H5 + * Method: H5export_attribute + * Signature: (Ljava/lang/String;JLjava/lang/String;I)V + */ +JNIEXPORT void JNICALL +Java_hdf_hdf5lib_H5_H5export_1attribute(JNIEnv *env, jclass clss, jstring file_export_name, jlong dset_id, + jstring attribute_name, jint binary_order) +{ + const char *file_export = NULL; + const char *object_name = NULL; + jboolean isCopy; + herr_t ret_val = FAIL; + hid_t attr_id = H5I_INVALID_HID; + FILE * stream = NULL; + + UNUSED(clss); + + if (NULL == file_export_name) + H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5export_dataset: file_export_name is NULL"); + + if (NULL == attribute_name) + H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5export_dataset: object_path is NULL"); + + PIN_JAVA_STRING(ENVONLY, attribute_name, object_name, &isCopy, + "H5export_dataset: object_path not pinned"); + + if ((attr_id = H5Aopen(dset_id, object_name, H5P_DEFAULT)) < 0) + H5_LIBRARY_ERROR(ENVONLY); + + PIN_JAVA_STRING(ENVONLY, file_export_name, file_export, NULL, + "H5export_dataset: file_export name not pinned"); + + if (NULL == (stream = HDfopen(file_export, "w+"))) + H5_JNI_FATAL_ERROR(ENVONLY, "HDfopen failed"); + + if ((ret_val = h5str_dump_simple_mem(ENVONLY, stream, attr_id, binary_order)) < 0) + H5_ASSERTION_ERROR(ENVONLY, "h5str_dump_simple_dset failed"); + + if (stream) { + HDfclose(stream); + stream = NULL; + } + +done: + if (stream) + HDfclose(stream); + if (file_export) + UNPIN_JAVA_STRING(ENVONLY, file_export_name, file_export); + if (object_name) + UNPIN_JAVA_STRING(ENVONLY, attribute_name, object_name); + if (attr_id >= 0) + H5Aclose(attr_id); +} /* end Java_hdf_hdf5lib_H5_H5export_1attribute */ + #ifdef __cplusplus } #endif diff --git a/java/src/jni/h5util.h b/java/src/jni/h5util.h index 7c5fb90..6c568e1 100644 --- a/java/src/jni/h5util.h +++ b/java/src/jni/h5util.h @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -41,13 +41,12 @@ extern void h5str_resize(h5str_t *str, size_t new_len); extern char * h5str_append(h5str_t *str, const char *cstr); extern size_t h5str_convert(JNIEnv *env, char **in_str, hid_t container, hid_t tid, void *out_buf, size_t out_buf_offset); -extern void h5str_sprint_reference(JNIEnv *env, h5str_t *out_str, hid_t container, void *ref_p); +extern int h5str_sprint_reference(JNIEnv *env, h5str_t *out_str, void *ref_p); extern size_t h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *in_buf, - size_t in_buf_len, int expand_data); + int expand_data); extern void h5str_array_free(char **strs, size_t len); extern int h5str_dump_simple_dset(JNIEnv *env, FILE *stream, hid_t dset, int binary_order); -extern int h5str_dump_region_blocks_data(JNIEnv *env, h5str_t *str, hid_t region, hid_t region_obj); -extern int h5str_dump_region_points_data(JNIEnv *env, h5str_t *str, hid_t region, hid_t region_obj); +extern int h5str_dump_simple_mem(JNIEnv *env, FILE *stream, hid_t attr, int binary_order); extern htri_t H5Tdetect_variable_str(hid_t tid); @@ -107,9 +106,16 @@ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Gget_1obj_1info_1max(JNIEnv *, jcla /* * Class: hdf_hdf5lib_H5 * Method: H5export_dataset - * Signature: (Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;I)V + * Signature: (Ljava/lang/String;JLjava/lang/String;I)V */ -JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5export_1dataset(JNIEnv *, jclass, jstring, jstring, jstring, - jint); +JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5export_1dataset(JNIEnv *, jclass, jstring, jlong, jstring, jint); + +/* + * Class: hdf_hdf5lib_H5 + * Method: H5export_attribute + * Signature: (Ljava/lang/String;JLjava/lang/String;I)V + */ +JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5export_1attribute(JNIEnv *, jclass, jstring, jlong, jstring, + jint); #endif /* H5UTIL_H__ */ diff --git a/java/src/jni/h5vlImp.c b/java/src/jni/h5vlImp.c index 1460e5d..40f8863 100644 --- a/java/src/jni/h5vlImp.c +++ b/java/src/jni/h5vlImp.c @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/jni/h5vlImp.h b/java/src/jni/h5vlImp.h index 4fbf577..a17807f 100644 --- a/java/src/jni/h5vlImp.h +++ b/java/src/jni/h5vlImp.h @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -14,8 +13,8 @@ #include <jni.h> /* Header for class hdf_hdf5lib_H5_H5VL */ -#ifndef _Included_hdf_hdf5lib_H5_H5VL -#define _Included_hdf_hdf5lib_H5_H5VL +#ifndef Included_hdf_hdf5lib_H5_H5VL +#define Included_hdf_hdf5lib_H5_H5VL #ifdef __cplusplus extern "C" { @@ -98,4 +97,4 @@ JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5VLunregister_1connector(JNIEnv *, j } /* end extern "C" */ #endif /* __cplusplus */ -#endif /* _Included_hdf_hdf5lib_H5_H5VL */ +#endif /* Included_hdf_hdf5lib_H5_H5VL */ diff --git a/java/src/jni/h5zImp.c b/java/src/jni/h5zImp.c index 5d9f442..d750ee8 100644 --- a/java/src/jni/h5zImp.c +++ b/java/src/jni/h5zImp.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/jni/h5zImp.h b/java/src/jni/h5zImp.h index 58b088b..3092ae6 100644 --- a/java/src/jni/h5zImp.h +++ b/java/src/jni/h5zImp.h @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -14,8 +13,8 @@ #include <jni.h> /* Header for class hdf_hdf5lib_H5_H5Z */ -#ifndef _Included_hdf_hdf5lib_H5_H5Z -#define _Included_hdf_hdf5lib_H5_H5Z +#ifndef Included_hdf_hdf5lib_H5_H5Z +#define Included_hdf_hdf5lib_H5_H5Z #ifdef __cplusplus extern "C" { @@ -47,4 +46,4 @@ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Zget_1filter_1info(JNIEnv *, jclass } /* end extern "C" */ #endif /* __cplusplus */ -#endif /* _Included_hdf_hdf5lib_H5_H5Z */ +#endif /* Included_hdf_hdf5lib_H5_H5Z */ diff --git a/java/src/jni/nativeData.c b/java/src/jni/nativeData.c index d2f00ec..9e63f4f 100644 --- a/java/src/jni/nativeData.c +++ b/java/src/jni/nativeData.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ diff --git a/java/src/jni/nativeData.h b/java/src/jni/nativeData.h index 012f73e..9bf313f 100644 --- a/java/src/jni/nativeData.h +++ b/java/src/jni/nativeData.h @@ -1,12 +1,11 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -14,8 +13,8 @@ #include <jni.h> /* Header for class hdf_hdf5lib_HDFNativeData */ -#ifndef _Included_hdf_hdf5lib_HDFNativeData -#define _Included_hdf_hdf5lib_HDFNativeData +#ifndef Included_hdf_hdf5lib_HDFNativeData +#define Included_hdf_hdf5lib_HDFNativeData #ifdef __cplusplus extern "C" { @@ -98,4 +97,4 @@ JNIEXPORT jbyteArray JNICALL Java_hdf_hdf5lib_HDFNativeData_byteToByte__B(JNIEnv } /* end extern "C" */ #endif /* __cplusplus */ -#endif /* _Included_hdf_hdf5lib_HDFNativeData */ +#endif /* Included_hdf_hdf5lib_HDFNativeData */ |